Variant report

Variant	rs57453427
Chromosome Location	chr3:50285930-50285931
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	POLR2A	chr3:50285878-50286059	Hela-S3	cervix:	n/a	n/a
2	RCOR1	chr3:50285900-50286140	Hela-S3	cervix:	n/a	n/a
3	STAT3	chr3:50285917-50286262	MCF10A-Er-Src	breast:	n/a	chr3:50286234-50286245 chr3:50286021-50286029 chr3:50286085-50286096
4	SMC3	chr3:50285877-50286157	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:50285682-50286810	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr3:50285644-50286634	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr3:50285804-50286119	HUVEC	blood vessel:	n/a	n/a
8	FOS	chr3:50285795-50286298	HUVEC	blood vessel:	n/a	chr3:50286073-50286084 chr3:50286075-50286083 chr3:50286071-50286082 chr3:50286074-50286085
9	MAZ	chr3:50285829-50286189	Hela-S3	cervix:	n/a	chr3:50285990-50286000
10	MAX	chr3:50285894-50286180	Hela-S3	cervix:	n/a	chr3:50285990-50286000
11	PBX3	chr3:50285858-50286331	SK-N-SH	brain:	n/a	chr3:50286054-50286063
12	FOS	chr3:50285900-50286249	MCF10A-Er-Src	breast:	n/a	chr3:50286073-50286084 chr3:50286075-50286083 chr3:50286071-50286082 chr3:50286074-50286085
13	CHD2	chr3:50285893-50286172	Hela-S3	cervix:	n/a	n/a
14	GTF2F1	chr3:50285922-50286274	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr3:50285606-50286308	HUVEC	blood vessel:	n/a	n/a
16	MYC	chr3:50285902-50286078	MCF-7	breast:	n/a	chr3:50285990-50286000
17	FOS	chr3:50285923-50286249	MCF10A-Er-Src	breast:	n/a	chr3:50286073-50286084 chr3:50286075-50286083 chr3:50286071-50286082 chr3:50286074-50286085
18	MYC	chr3:50285899-50286178	HUVEC	blood vessel:	n/a	chr3:50285990-50286000
19	POLR2A	chr3:50285870-50286226	HCT-116	colon:	n/a	n/a
20	PBX3	chr3:50285783-50286252	SK-N-SH	brain:	n/a	chr3:50286054-50286063

No.	Distal block	Cell Line	Cell type
1	chr3:50283654..50286380-chr3:50314106..50317023,3	K562	blood:
2	chr3:50285794..50287814-chr3:50306650..50309079,2	MCF-7	breast:
3	chr3:50284317..50286473-chr3:50288489..50290077,2	K562	blood:
4	chr3:50284602..50287815-chr3:50290818..50293169,4	K562	blood:
5	chr3:50283737..50287668-chr3:50290117..50294367,4	K562	blood:
6	chr3:50285711..50287237-chr3:50303937..50306020,2	MCF-7	breast:
7	chr3:50272949..50274999-chr3:50285398..50287724,2	MCF-7	breast:

Variant related genes	Relation type
GNAI2	TF binding region
ENSG00000114353	Chromatin interaction
ENSG00000232352	Chromatin interaction
ENSG00000179564	Chromatin interaction
ENSG00000012171	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11914549	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11916258	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1894324	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35742391	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56287038	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58415636	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61382127	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6446203	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6768830	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629917	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7636862	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7641224	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs886075	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9836046	0.95[EUR][1000 genomes]
rs9851719	1.00[EUR][1000 genomes]
rs9875873	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9878345	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50276200-50286600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:50276200-50287000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:50276400-50294400	Genic enhancers	Lung	lung
4	chr3:50278600-50287400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:50278800-50286800	Enhancers	NHDF-Ad	bronchial
6	chr3:50283400-50293200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:50283800-50286200	Enhancers	Brain Hippocampus Middle	brain
8	chr3:50283800-50286400	Weak transcription	Ovary	ovary
9	chr3:50283800-50287200	Enhancers	Gastric	stomach
10	chr3:50283800-50289000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:50283800-50289400	Enhancers	Left Ventricle	heart
12	chr3:50283800-50294000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:50284000-50286600	Genic enhancers	Fetal Stomach	stomach
14	chr3:50284000-50286800	Genic enhancers	Fetal Intestine Small	intestine
15	chr3:50284000-50289000	Enhancers	Brain Cingulate Gyrus	brain
16	chr3:50284000-50289200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr3:50284000-50289400	Genic enhancers	Primary B cells from peripheral blood	blood
18	chr3:50284200-50286000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:50284200-50286600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:50284200-50286600	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr3:50284200-50286800	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr3:50284200-50287000	Genic enhancers	Fetal Intestine Large	intestine
23	chr3:50284200-50287400	Genic enhancers	Primary monocytes fromperipheralblood	blood
24	chr3:50284200-50287400	Weak transcription	Pancreas	Pancrea
25	chr3:50284200-50287800	Enhancers	HMEC	breast
26	chr3:50284200-50287800	Genic enhancers	NHLF	lung
27	chr3:50284200-50288200	Enhancers	Right Ventricle	heart
28	chr3:50284200-50288600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr3:50284200-50289600	Genic enhancers	Duodenum Smooth Muscle	Duodenum
30	chr3:50284200-50289600	Enhancers	Right Atrium	heart
31	chr3:50284200-50289800	Enhancers	Stomach Mucosa	stomach
32	chr3:50284200-50297000	Genic enhancers	Fetal Muscle Trunk	muscle
33	chr3:50284400-50286000	Weak transcription	Brain Substantia Nigra	brain
34	chr3:50284400-50286400	Genic enhancers	Rectal Mucosa Donor 29	rectum
35	chr3:50284400-50287200	Enhancers	Colonic Mucosa	Colon
36	chr3:50284400-50287800	Genic enhancers	Stomach Smooth Muscle	stomach
37	chr3:50284400-50288200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:50284400-50289400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr3:50284400-50289400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:50284400-50290800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:50284400-50292000	Weak transcription	Fetal Brain Male	brain
42	chr3:50284400-50293000	Genic enhancers	Primary T cells fromperipheralblood	blood
43	chr3:50284400-50295000	Genic enhancers	Spleen	Spleen
44	chr3:50284400-50295800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:50284400-50297000	Genic enhancers	Fetal Muscle Leg	muscle
46	chr3:50284600-50286000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:50284600-50286000	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr3:50284600-50286200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr3:50284600-50287400	Genic enhancers	Primary B cells from cord blood	blood
50	chr3:50284600-50287400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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