Variant report

Variant	rs9847853
Chromosome Location	chr3:50250215-50250216
allele	C/T
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	CTCF	chr3:50250019-50250360	H1-hESC	embryonic stem cell:	n/a	chr3:50250148-50250157
2	CTCF	chr3:50250080-50250230	NHDF-neo	bronchial:	n/a	chr3:50250148-50250157
3	CTCF	chr3:50250100-50250250	GM12867	blood:	n/a	chr3:50250148-50250157
4	CTCF	chr3:50250029-50250263	H1-hESC	embryonic stem cell:	n/a	chr3:50250148-50250157
5	CTCF	chr3:50250080-50250230	GM12878	blood:	n/a	chr3:50250148-50250157
6	CTCF	chr3:50250088-50250227	Gliobla	brain:	n/a	chr3:50250148-50250157
7	CTCF	chr3:50250072-50250224	HepG2	liver:	n/a	chr3:50250148-50250157
8	CTCF	chr3:50250100-50250250	Hela-S3	cervix:	n/a	chr3:50250148-50250157
9	CTCF	chr3:50250100-50250250	GM12869	blood:	n/a	chr3:50250148-50250157
10	CTCF	chr3:50250100-50250250	HEK293	kidney:	n/a	chr3:50250148-50250157
11	CTCF	chr3:50250080-50250230	A549	lung:	n/a	chr3:50250148-50250157
12	CTCF	chr3:50250080-50250230	GM12870	blood:	n/a	chr3:50250148-50250157
13	CTCF	chr3:50250100-50250250	GM12875	blood:	n/a	chr3:50250148-50250157
14	CTCF	chr3:50250115-50250224	GM12878	blood:	n/a	chr3:50250148-50250157
15	POLR2A	chr3:50249560-50250292	HepG2	liver:	n/a	n/a
16	RAD21	chr3:50250023-50250258	HepG2	liver:	n/a	n/a
17	ZNF143	chr3:50250028-50250236	H1-hESC	embryonic stem cell:	n/a	n/a
18	RAD21	chr3:50250040-50250283	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr3:50250020-50250251	K562	blood:	n/a	chr3:50250148-50250157
20	CTCF	chr3:50250120-50250270	WI-38	lung:	n/a	chr3:50250148-50250157
21	CTCF	chr3:50250100-50250250	GM12872	blood:	n/a	chr3:50250148-50250157
22	CTCF	chr3:50250100-50250250	GM12871	blood:	n/a	chr3:50250148-50250157
23	CTCF	chr3:50250080-50250230	GM12864	blood:	n/a	chr3:50250148-50250157
24	CTCF	chr3:50250080-50250230	K562	blood:	n/a	chr3:50250148-50250157
25	CTCF	chr3:50250100-50250250	HA-sp	spinal cord:	n/a	chr3:50250148-50250157
26	CTCF	chr3:50250120-50250270	GM12864	blood:	n/a	chr3:50250148-50250157
27	CTCF	chr3:50250100-50250250	HAc	cerebellar:	n/a	chr3:50250148-50250157
28	CTCF	chr3:50250080-50250230	HCM	heart:	n/a	chr3:50250148-50250157
29	CTCF	chr3:50250080-50250230	GM12869	blood:	n/a	chr3:50250148-50250157
30	POLR2A	chr3:50249510-50250579	HepG2	liver:	n/a	n/a
31	RAD21	chr3:50249995-50250271	HepG2	liver:	n/a	n/a
32	CTCF	chr3:50250080-50250230	GM12866	blood:	n/a	chr3:50250148-50250157
33	CTCF	chr3:50250080-50250230	HUVEC	blood vessel:	n/a	chr3:50250148-50250157
34	CTCF	chr3:50250063-50250215	Hela-S3	cervix:	n/a	chr3:50250148-50250157
35	CTCF	chr3:50250082-50250218	GM12891	blood:	n/a	chr3:50250148-50250157
36	CTCF	chr3:50250080-50250230	Hela-S3	cervix:	n/a	chr3:50250148-50250157
37	CTCF	chr3:50250100-50250250	GM12873	blood:	n/a	chr3:50250148-50250157
38	CTCF	chr3:50250090-50250225	K562	blood:	n/a	chr3:50250148-50250157
39	CTCF	chr3:50250140-50250290	GM12874	blood:	n/a	chr3:50250148-50250157
40	CTCF	chr3:50250100-50250250	HCFaa	heart:	n/a	chr3:50250148-50250157
41	CTCF	chr3:50250100-50250250	HPAF	blood vessel:	n/a	chr3:50250148-50250157
42	MXI1	chr3:50250039-50250239	HepG2	liver:	n/a	n/a
43	CTCF	chr3:50250100-50250250	GM12874	blood:	n/a	chr3:50250148-50250157
44	CTCF	chr3:50250013-50250239	HepG2	liver:	n/a	chr3:50250148-50250157
45	CTCF	chr3:50250080-50250230	GM06990	blood:	n/a	chr3:50250148-50250157

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50192296..50194939-chr3:50249024..50251432,2	MCF-7	breast:

Variant related genes	Relation type
SLC38A3	TF binding region
ENSG00000235016	Chromatin interaction
ENSG00000001617	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs4141407	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs61669412	1.00[EUR][1000 genomes]
rs7611366	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9847587	1.00[EUR][1000 genomes]
rs9867538	0.97[AFR][1000 genomes];1.00[AMR][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:41 , 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	chr3:50244400-50263800	Weak transcription	Right Ventricle	heart
6	chr3:50246600-50250600	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:50246800-50251400	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr3:50247400-50250400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:50247400-50264400	Weak transcription	Ovary	ovary
10	chr3:50247600-50250600	Weak transcription	Fetal Brain Female	brain
11	chr3:50248000-50250400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr3:50248200-50250600	Enhancers	Psoas Muscle	Psoas
13	chr3:50248200-50253000	Enhancers	Brain Hippocampus Middle	brain
14	chr3:50248400-50255200	Weak transcription	Spleen	Spleen
15	chr3:50249000-50250600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:50249000-50251400	Enhancers	Liver	Liver
17	chr3:50249000-50259000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:50249200-50250800	Enhancers	Adipose Nuclei	Adipose
19	chr3:50249200-50251600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:50249200-50252800	Enhancers	Brain Anterior Caudate	brain
21	chr3:50249400-50250400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
22	chr3:50249400-50250400	Enhancers	Brain Cingulate Gyrus	brain
23	chr3:50249400-50251600	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr3:50249400-50251800	Enhancers	Brain Angular Gyrus	brain
25	chr3:50249400-50252400	Enhancers	Brain Substantia Nigra	brain
26	chr3:50249400-50252600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:50249600-50250400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:50249600-50250400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:50249600-50250400	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr3:50249600-50251800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:50249600-50252800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr3:50249600-50253800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr3:50249800-50250800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:50249800-50251000	Weak transcription	Stomach Mucosa	stomach
35	chr3:50249800-50255000	Weak transcription	HMEC	breast
36	chr3:50250000-50250600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:50250000-50252000	Genic enhancers	HepG2	liver
38	chr3:50250000-50253000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:50250000-50256400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:50250200-50251400	Enhancers	Brain Germinal Matrix	brain
41	chr3:50250200-50255400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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