Variant report

Variant	rs62260792
Chromosome Location	chr3:50248427-50248428
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RXRA	chr3:50247747-50248544	HepG2	liver:	n/a	chr3:50248286-50248302
2	YY1	chr3:50248148-50248761	H1-hESC	embryonic stem cell:	n/a	chr3:50248737-50248748
3	MAZ	chr3:50247847-50248912	HepG2	liver:	n/a	chr3:50248033-50248042 chr3:50248131-50248147 chr3:50248142-50248151
4	CHD2	chr3:50248132-50248778	HepG2	liver:	n/a	n/a
5	NFIC	chr3:50247769-50248645	HepG2	liver:	n/a	n/a
6	EP300	chr3:50247777-50248496	HepG2	liver:	n/a	n/a
7	TEAD4	chr3:50247868-50248467	HepG2	liver:	n/a	n/a
8	ZNF143	chr3:50248420-50248610	H1-hESC	embryonic stem cell:	n/a	n/a
9	GATA3	chr3:50248056-50248455	MCF-7	breast:	n/a	chr3:50248197-50248207 chr3:50248199-50248216 chr3:50248198-50248205 chr3:50248198-50248207
10	ZEB1	chr3:50247773-50249085	HepG2	liver:	n/a	n/a
11	MYBL2	chr3:50247679-50248901	HepG2	liver:	n/a	n/a
12	CTCF	chr3:50248401-50248515	H1-hESC	embryonic stem cell:	n/a	n/a
13	HEY1	chr3:50247085-50248970	HepG2	liver:	n/a	n/a
14	RCOR1	chr3:50247766-50248795	HepG2	liver:	n/a	n/a
15	EP300	chr3:50247784-50248868	HepG2	liver:	n/a	n/a
16	EP300	chr3:50247714-50248488	HepG2	liver:	n/a	n/a
17	ZEB1	chr3:50247640-50249020	HepG2	liver:	n/a	n/a
18	CEBPD	chr3:50247788-50248837	HepG2	liver:	n/a	n/a
19	RAD21	chr3:50248309-50248507	HepG2	liver:	n/a	n/a
20	POU5F1	chr3:50248404-50248683	H1-hESC	embryonic stem cell:	n/a	chr3:50248570-50248584 chr3:50248570-50248584
21	NFIC	chr3:50247861-50248497	HepG2	liver:	n/a	n/a
22	HNF4A	chr3:50247719-50248995	HepG2	liver:	n/a	chr3:50248767-50248782 chr3:50247964-50247979 chr3:50248768-50248780 chr3:50248767-50248782 chr3:50248767-50248781 chr3:50247987-50248002 chr3:50248767-50248782 chr3:50248768-50248781 chr3:50248773-50248781 chr3:50248768-50248780 chr3:50248767-50248782 chr3:50248774-50248782
23	MAX	chr3:50248012-50248873	HepG2	liver:	n/a	chr3:50248033-50248042 chr3:50248131-50248147 chr3:50248142-50248151
24	POLR2A	chr3:50247154-50249010	HepG2	liver:	n/a	n/a
25	MYBL2	chr3:50247690-50249028	HepG2	liver:	n/a	n/a
26	FOXA1	chr3:50247738-50248970	HepG2	liver:	n/a	n/a
27	JUN	chr3:50248006-50248431	HepG2	liver:	n/a	chr3:50248174-50248185
28	MBD4	chr3:50247937-50248528	HepG2	liver:	n/a	n/a
29	POLR2A	chr3:50247645-50248464	HepG2	liver:	n/a	n/a
30	YY1	chr3:50247948-50248969	HepG2	liver:	n/a	chr3:50248737-50248748
31	HDAC2	chr3:50247796-50248473	HepG2	liver:	n/a	chr3:50247950-50247964 chr3:50248142-50248151 chr3:50247998-50248017
32	BRCA1	chr3:50248132-50248534	HepG2	liver:	n/a	n/a
33	POLR2A	chr3:50247042-50248992	HepG2	liver:	n/a	n/a
34	BHLHE40	chr3:50247825-50248808	HepG2	liver:	n/a	n/a
35	FOXA1	chr3:50247772-50248465	HepG2	liver:	n/a	n/a
36	SP1	chr3:50247710-50249016	HepG2	liver:	n/a	chr3:50248739-50248753 chr3:50248746-50248760
37	SIN3AK20	chr3:50248400-50248794	H1-hESC	embryonic stem cell:	n/a	n/a
38	HNF4A	chr3:50247842-50248439	HepG2	liver:	n/a	chr3:50247964-50247979 chr3:50247987-50248002
39	HNF4G	chr3:50247753-50248452	HepG2	liver:	n/a	n/a
40	HEY1	chr3:50247113-50248969	HepG2	liver:	n/a	n/a
41	RXRA	chr3:50247804-50248470	HepG2	liver:	n/a	chr3:50248286-50248302
42	HNF4A	chr3:50247783-50248435	HepG2	liver:	n/a	chr3:50247964-50247979 chr3:50247987-50248002
43	FOXA1	chr3:50247877-50248499	HepG2	liver:	n/a	n/a
44	TBP	chr3:50248369-50248632	H1-hESC	embryonic stem cell:	n/a	n/a
45	FOSL2	chr3:50247718-50248512	HepG2	liver:	n/a	chr3:50247968-50247979 chr3:50248174-50248185
46	POLR2A	chr3:50247212-50248568	HepG2	liver:	n/a	n/a
47	JUND	chr3:50247860-50248463	HepG2	liver:	n/a	chr3:50247968-50247979 chr3:50248174-50248185
48	POLR2A	chr3:50247325-50248881	HepG2	liver:	n/a	n/a
49	JUND	chr3:50247885-50248481	HepG2	liver:	n/a	chr3:50247968-50247979 chr3:50248174-50248185
50	MXI1	chr3:50247787-50248934	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50241794..50243896-chr3:50246798..50250002,3	MCF-7	breast:
2	chr3:50246100..50248921-chr3:50262200..50264604,3	MCF-7	breast:

Variant related genes	Relation type
SLC38A3	TF binding region
ENSG00000188338	Chromatin interaction
ENSG00000114353	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12486832	1.00[AFR][1000 genomes]
rs12636449	0.82[EUR][1000 genomes]
rs60429865	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62260773	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62260798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260813	1.00[AFR][1000 genomes]
rs62260817	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
10	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
11	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
12	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
13	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
14	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
15	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
16	nsv460529	chr3:50178011-50324672	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
17	nsv460530	chr3:50178011-50324672	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv590252	chr3:50178011-50324672	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
19	nsv1002916	chr3:50187646-50311666	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
20	nsv536564	chr3:50187646-50311666	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
21	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
22	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
23	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
24	nsv590253	chr3:50196418-50337422	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
25	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
26	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
27	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
28	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
29	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
30	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50244000-50251200	Enhancers	Pancreas	Pancrea
2	chr3:50244000-50254600	Weak transcription	Esophagus	oesophagus
3	chr3:50244000-50263800	Weak transcription	Right Atrium	heart
4	chr3:50244200-50263800	Weak transcription	Left Ventricle	heart
5	chr3:50244400-50249600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:50244400-50263800	Weak transcription	Right Ventricle	heart
7	chr3:50246400-50248600	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr3:50246400-50249200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:50246400-50249400	Weak transcription	Brain Angular Gyrus	brain
10	chr3:50246400-50249600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:50246600-50249400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:50246600-50249400	Weak transcription	Brain Substantia Nigra	brain
13	chr3:50246600-50250600	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:50246800-50251400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr3:50247200-50248800	Enhancers	Duodenum Mucosa	Duodenum
16	chr3:50247200-50249200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr3:50247400-50248800	Enhancers	Stomach Mucosa	stomach
18	chr3:50247400-50249200	Weak transcription	Adipose Nuclei	Adipose
19	chr3:50247400-50250000	Enhancers	Fetal Intestine Small	intestine
20	chr3:50247400-50250200	Enhancers	Fetal Intestine Large	intestine
21	chr3:50247400-50250400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:50247400-50264400	Weak transcription	Ovary	ovary
23	chr3:50247600-50248800	Flanking Active TSS	HepG2	liver
24	chr3:50247600-50249000	Enhancers	Small Intestine	intestine
25	chr3:50247600-50249400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:50247600-50250600	Weak transcription	Fetal Brain Female	brain
27	chr3:50247800-50248600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr3:50247800-50248800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr3:50247800-50248800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:50247800-50249000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:50247800-50249400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:50247800-50249400	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr3:50248000-50249200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:50248000-50249600	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr3:50248000-50250000	Enhancers	H1 Cell Line	embryonic stem cell
36	chr3:50248000-50250400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr3:50248200-50248600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr3:50248200-50248800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr3:50248200-50248800	Enhancers	Brain Anterior Caudate	brain
40	chr3:50248200-50250600	Enhancers	Psoas Muscle	Psoas
41	chr3:50248200-50253000	Enhancers	Brain Hippocampus Middle	brain
42	chr3:50248400-50248600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:50248400-50248600	Flanking Active TSS	Liver	Liver
44	chr3:50248400-50255200	Weak transcription	Spleen	Spleen

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