Variant report

Variant	rs557827745
Chromosome Location	chr3:50191757-50191758
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	REST	chr3:50191706-50193577	H1-neurons	neurons:	n/a	chr3:50192632-50192645 chr3:50193092-50193102 chr3:50192628-50192648 chr3:50193114-50193124 chr3:50192001-50192014 chr3:50192628-50192648
2	ZBTB7A	chr3:50191749-50192441	ECC-1	luminal epithelium:	n/a	n/a
3	RAD21	chr3:50191709-50192127	MCF-7	breast:	n/a	chr3:50192009-50192028 chr3:50191850-50191864 chr3:50192011-50192023
4	POLR2A	chr3:50191660-50191772	MCF-7	breast:	n/a	n/a
5	RAD21	chr3:50191744-50192242	MCF-7	breast:	n/a	chr3:50192009-50192028 chr3:50191850-50191864 chr3:50192011-50192023
6	RAD21	chr3:50191734-50192208	SK-N-SH_RA	brain:	n/a	chr3:50192009-50192028 chr3:50191850-50191864 chr3:50192011-50192023
7	CTCF	chr3:50191720-50191870	Caco-2	colon:	n/a	n/a
8	RAD21	chr3:50191454-50192384	SK-N-SH	brain:	n/a	chr3:50192009-50192028 chr3:50191850-50191864 chr3:50192011-50192023
9	CTCF	chr3:50191640-50191790	GM12871	blood:	n/a	n/a
10	SMC3	chr3:50191268-50193403	SK-N-SH	brain:	n/a	chr3:50191660-50191668 chr3:50192013-50192023 chr3:50192717-50192727 chr3:50192013-50192027
11	CTCF	chr3:50191660-50191810	HFF-Myc	foreskin:	n/a	n/a
12	CTCF	chr3:50191640-50193044	SK-N-SH	brain:	n/a	chr3:50192716-50192726 chr3:50192006-50192027 chr3:50192013-50192026 chr3:50192011-50192029 chr3:50192714-50192727
13	CTCF	chr3:50191660-50191810	HA-sp	spinal cord:	n/a	n/a
14	RAD21	chr3:50191706-50192163	H1-hESC	embryonic stem cell:	n/a	chr3:50192009-50192028 chr3:50191850-50191864 chr3:50192011-50192023

No.	Distal block	Cell Line	Cell type
1	chr3:50189363..50191977-chr3:50309007..50311899,2	MCF-7	breast:
2	chr3:50191641..50194297-chr3:50220054..50223610,4	MCF-7	breast:
3	chr3:50159119..50159942-chr3:50191580..50192142,2	MCF-7	breast:
4	chr3:50190470..50194491-chr3:50196225..50201802,7	K562	blood:
5	chr3:50158688..50160030-chr3:50191274..50192403,3	MCF-7	breast:
6	chr3:50191627..50193691-chr3:50209687..50211278,2	MCF-7	breast:
7	chr3:50191338..50193199-chr3:50263040..50265048,2	MCF-7	breast:
8	chr3:50191401..50200098-chr3:50206213..50213809,14	MCF-7	breast:

Variant related genes	Relation type
SEMA3F	TF binding region
ENSG00000001617	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000207922	Chromatin interaction
ENSG00000114353	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:26 , 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	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	esv3323037	chr3:50190548-50194846	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
26	esv3356010	chr3:50191398-50194246	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50177200-50191800	Weak transcription	Right Ventricle	heart
2	chr3:50183600-50192000	Enhancers	Esophagus	oesophagus
3	chr3:50187600-50191800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:50187600-50192000	Enhancers	HMEC	breast
5	chr3:50187600-50192400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:50188800-50191800	Enhancers	Spleen	Spleen
7	chr3:50189200-50191800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:50189200-50191800	Weak transcription	Liver	Liver
9	chr3:50189400-50191800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:50189400-50191800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:50189600-50191800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:50189600-50191800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:50189600-50193000	Weak transcription	Fetal Lung	lung
14	chr3:50190000-50193000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:50190800-50192000	Enhancers	Fetal Kidney	kidney
16	chr3:50191000-50191800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:50191000-50192000	Enhancers	Gastric	stomach
18	chr3:50191000-50192000	Enhancers	Lung	lung
19	chr3:50191200-50191800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:50191200-50191800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:50191200-50192400	Weak transcription	NHEK	skin
22	chr3:50191400-50191800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
23	chr3:50191400-50191800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:50191400-50191800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:50191400-50191800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr3:50191400-50191800	Enhancers	Hela-S3	cervix
27	chr3:50191400-50191800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
28	chr3:50191400-50192000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:50191400-50192000	Enhancers	Fetal Brain Male	brain
30	chr3:50191400-50192000	Enhancers	Fetal Heart	heart
31	chr3:50191400-50192000	Bivalent Enhancer	Fetal Stomach	stomach
32	chr3:50191600-50191800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
33	chr3:50191600-50191800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
34	chr3:50191600-50191800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:50191600-50191800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:50191600-50191800	Bivalent Enhancer	Primary B cells from cord blood	blood
37	chr3:50191600-50191800	Enhancers	Primary hematopoietic stem cells	blood
38	chr3:50191600-50191800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
39	chr3:50191600-50191800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr3:50191600-50191800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:50191600-50191800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
42	chr3:50191600-50191800	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:50191600-50191800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:50191600-50191800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
45	chr3:50191600-50191800	Enhancers	Colonic Mucosa	Colon
46	chr3:50191600-50191800	Enhancers	Duodenum Mucosa	Duodenum
47	chr3:50191600-50191800	Flanking Active TSS	Fetal Brain Female	brain
48	chr3:50191600-50191800	Enhancers	Pancreas	Pancrea
49	chr3:50191600-50191800	Enhancers	Stomach Smooth Muscle	stomach
50	chr3:50191600-50191800	Enhancers	HUVEC	blood vessel

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