Variant report

Variant	rs1281120
Chromosome Location	chr4:8201828-8201829
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	chr4:8200632-8202730	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:8200369-8205269	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:8201816-8202162	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:8201586-8203464	HUVEC	blood vessel:	n/a	n/a
5	EBF1	chr4:8201721-8202298	GM12878	blood:	n/a	chr4:8201779-8201790
6	MXI1	chr4:8200576-8201975	HepG2	liver:	n/a	n/a
7	CTCF	chr4:8201700-8201850	GM12872	blood:	n/a	chr4:8201708-8201716
8	POLR2A	chr4:8200634-8201946	HUVEC	blood vessel:	n/a	n/a
9	RCOR1	chr4:8201768-8203775	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:8201798-8202660	GM12891	blood:	n/a	n/a
11	POLR2A	chr4:8200443-8205116	GM18505	blood:	n/a	n/a
12	MAX	chr4:8201791-8202245	A549	lung:	n/a	n/a
13	POLR2A	chr4:8201774-8204219	GM12878	blood:	n/a	n/a
14	POLR2A	chr4:8200122-8204378	GM18526	blood:	n/a	n/a
15	POLR2A	chr4:8200506-8204225	GM19193	blood:	n/a	n/a
16	POLR2A	chr4:8200695-8203509	HUVEC	blood vessel:	n/a	n/a
17	EBF1	chr4:8201574-8202402	GM12878	blood:	n/a	chr4:8201779-8201790
18	POLR2A	chr4:8200565-8203402	PFSK-1	brain:	n/a	n/a
19	MAX	chr4:8200588-8202244	A549	lung:	n/a	n/a
20	CHD2	chr4:8201619-8202656	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:8201781-8202689	HepG2	liver:	n/a	n/a
22	POLR2A	chr4:8200354-8202631	Raji	blood:	n/a	n/a
23	POLR2A	chr4:8201572-8203307	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr4:8201560-8202333	GM12891	blood:	n/a	n/a
25	PAX5	chr4:8201781-8202114	GM12892	blood:	n/a	n/a
26	MYC	chr4:8201780-8202069	HUVEC	blood vessel:	n/a	n/a
27	SMC3	chr4:8201717-8201900	GM12878	blood:	n/a	n/a
28	POU2F2	chr4:8201502-8202528	GM12878	blood:	n/a	n/a
29	POLR2A	chr4:8200430-8203861	HUVEC	blood vessel:	n/a	n/a
30	CTCF	chr4:8201760-8201910	GM12873	blood:	n/a	n/a
31	WRNIP1	chr4:8201617-8204724	GM12878	blood:	n/a	n/a
32	MTA3	chr4:8200020-8205097	GM12878	blood:	n/a	n/a
33	POLR2A	chr4:8200473-8203690	GM12878	blood:	n/a	n/a
34	POLR2A	chr4:8200278-8205230	GM12891	blood:	n/a	n/a
35	CTCF	chr4:8201812-8202432	GM12878	blood:	n/a	n/a
36	HMGN3	chr4:8201785-8202114	K562	blood:	n/a	n/a
37	RELA	chr4:8201644-8202717	GM19099	blood:	n/a	n/a
38	CHD1	chr4:8200388-8203794	GM12878	blood:	n/a	n/a
39	TBP	chr4:8201674-8203636	GM12878	blood:	n/a	n/a
40	SIN3A	chr4:8201784-8202784	GM12878	blood:	n/a	chr4:8202267-8202280 chr4:8201906-8201919 chr4:8201958-8201967
41	CTCF	chr4:8201820-8202090	GM12872	blood:	n/a	n/a
42	POLR2A	chr4:8201709-8205132	GM12878	blood:	n/a	n/a
43	POLR2A	chr4:8201524-8202598	GM12892	blood:	n/a	n/a
44	POLR2A	chr4:8201615-8202546	GM12892	blood:	n/a	n/a
45	MAX	chr4:8201601-8202157	A549	lung:	n/a	n/a
46	CTCF	chr4:8201800-8201950	GM12874	blood:	n/a	n/a
47	TCF3	chr4:8201756-8202315	GM12878	blood:	n/a	n/a
48	POLR2A	chr4:8200450-8204220	GM12878	blood:	n/a	n/a
49	ZEB1	chr4:8201756-8202242	GM12878	blood:	n/a	n/a
50	YY1	chr4:8201782-8202577	GM12878	blood:	n/a	chr4:8202319-8202338

No.	Distal block	Cell Line	Cell type
1	chr4:8199393..8202510-chr4:8203198..8206188,4	MCF-7	breast:
2	chr4:8201008..8201849-chr4:156775894..156776553,2	MCF-7	breast:
3	chr4:8181697..8186152-chr4:8199354..8203571,7	MCF-7	breast:
4	chr4:8158369..8164233-chr4:8200767..8204083,4	MCF-7	breast:
5	chr4:8199821..8202591-chr4:8203028..8206014,3	K562	blood:

Variant related genes	Relation type
SH3TC1	TF binding region
ENSG00000151790	Chromatin interaction
ENSG00000163995	Chromatin interaction
ENSG00000125089	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1078701	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1281114	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1281115	1.00[CEU][hapmap]
rs1281118	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1281119	0.92[EUR][1000 genomes]
rs1281123	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1678261	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1678262	1.00[CEU][hapmap]
rs1678310	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3115217	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878591	chr4:8063501-8207083	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1010809	chr4:8097627-8292324	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv878593	chr4:8125788-8233341	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv461216	chr4:8154534-8276411	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv593626	chr4:8154534-8276411	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv878594	chr4:8154534-8286916	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv878595	chr4:8154534-8390646	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv470012	chr4:8171401-8233341	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv878596	chr4:8171401-8254784	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv878597	chr4:8171401-8294196	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv829853	chr4:8172065-8320868	Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
13	nsv869928	chr4:8195069-8214848	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv878598	chr4:8195705-8254784	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv878599	chr4:8195705-8293398	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	esv2763338	chr4:8199091-8260812	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	esv1831794	chr4:8199833-8233341	Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8185200-8202600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:8195800-8204200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:8200000-8202000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:8200000-8202200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
5	chr4:8200000-8203200	Enhancers	Fetal Heart	heart
6	chr4:8200000-8204000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr4:8200000-8206000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:8200200-8202200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr4:8200200-8203200	Flanking Active TSS	Colonic Mucosa	Colon
10	chr4:8200200-8203800	Active TSS	Rectal Smooth Muscle	rectum
11	chr4:8200200-8204000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:8200200-8204000	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr4:8200200-8204800	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr4:8200200-8205800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:8200400-8202200	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr4:8200400-8203000	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr4:8200400-8203000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr4:8200400-8203600	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr4:8200400-8203600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr4:8200400-8203600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:8200400-8204000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
22	chr4:8200400-8204000	Active TSS	Brain Anterior Caudate	brain
23	chr4:8200400-8204400	Flanking Active TSS	Fetal Thymus	thymus
24	chr4:8200600-8202000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:8200600-8202400	Flanking Active TSS	Spleen	Spleen
26	chr4:8200600-8202600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr4:8200600-8202800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr4:8200600-8202800	Flanking Active TSS	Pancreas	Pancrea
29	chr4:8200600-8202800	Enhancers	K562	blood
30	chr4:8200600-8203000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:8200600-8203000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr4:8200600-8203000	Flanking Active TSS	Osteobl	bone
33	chr4:8200600-8203200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:8200600-8203200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:8200600-8203200	Enhancers	Placenta Amnion	Placenta Amnion
36	chr4:8200600-8203400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:8200600-8203600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr4:8200600-8203800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr4:8200600-8204000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr4:8200600-8204000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr4:8200600-8205200	Flanking Active TSS	Dnd41	blood
42	chr4:8200800-8202000	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr4:8200800-8202000	Active TSS	HUVEC	blood vessel
44	chr4:8200800-8202600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:8200800-8202800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:8200800-8202800	Active TSS	Fetal Kidney	kidney
47	chr4:8200800-8203000	Flanking Active TSS	Fetal Stomach	stomach
48	chr4:8200800-8203000	Active TSS	Hela-S3	cervix
49	chr4:8200800-8203200	Active TSS	Brain Substantia Nigra	brain
50	chr4:8200800-8203400	Flanking Active TSS	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links