Variant report

Variant	rs2994809
Chromosome Location	chr1:120351977-120351978
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	STAT3	chr1:120351756-120351997	GM12878	blood:	n/a	n/a
2	RAD21	chr1:120351580-120352010	H1-hESC	embryonic stem cell:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
3	RAD21	chr1:120351611-120352018	SK-N-SH_RA	brain:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
4	RAD21	chr1:120351573-120351990	H1-hESC	embryonic stem cell:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
5	SRF	chr1:120351572-120352107	HCT-116	colon:	n/a	n/a
6	RAD21	chr1:120351532-120352119	MCF-7	breast:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
7	CTCF	chr1:120351579-120351991	K562	blood:	n/a	chr1:120351770-120351791 chr1:120351771-120351784 chr1:120351771-120351784 chr1:120351768-120351786 chr1:120351769-120351785
8	CTCF	chr1:120351414-120352009	K562	blood:	n/a	chr1:120351770-120351791 chr1:120351771-120351784 chr1:120351771-120351784 chr1:120351768-120351786 chr1:120351769-120351785
9	RAD21	chr1:120351205-120352264	SK-N-SH	brain:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
10	RAD21	chr1:120351572-120352067	IMR90	lung:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
11	SRF	chr1:120351595-120351999	ECC-1	luminal epithelium:	n/a	n/a
12	RAD21	chr1:120351431-120352143	HCT-116	colon:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
13	RAD21	chr1:120351492-120352089	HCT-116	colon:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
14	RAD21	chr1:120351553-120352022	A549	lung:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
15	MAZ	chr1:120351634-120352015	HepG2	liver:	n/a	n/a
16	SMC3	chr1:120351579-120352158	GM12878	blood:	n/a	chr1:120351770-120351784
17	CTCF	chr1:120351459-120352099	MCF-7	breast:	n/a	chr1:120351770-120351791 chr1:120351771-120351784 chr1:120351771-120351784 chr1:120351768-120351786 chr1:120351769-120351785
18	ZC3H11A	chr1:120351673-120352022	K562	blood:	n/a	n/a
19	RAD21	chr1:120351521-120352072	ECC-1	luminal epithelium:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
20	MAFK	chr1:120351626-120352068	Hela-S3	cervix:	n/a	n/a
21	MAFF	chr1:120351617-120352018	K562	blood:	n/a	n/a
22	CTCF	chr1:120351515-120352087	HCT-116	colon:	n/a	chr1:120351770-120351791 chr1:120351771-120351784 chr1:120351771-120351784 chr1:120351768-120351786 chr1:120351769-120351785
23	SMC3	chr1:120351541-120352004	HepG2	liver:	n/a	chr1:120351770-120351784
24	RAD21	chr1:120351497-120352061	MCF-7	breast:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
25	MXI1	chr1:120351611-120352032	GM12878	blood:	n/a	n/a
26	CTCF	chr1:120351522-120352111	MCF-7	breast:	n/a	chr1:120351770-120351791 chr1:120351771-120351784 chr1:120351771-120351784 chr1:120351768-120351786 chr1:120351769-120351785
27	STAT3	chr1:120351747-120352213	MCF10A-Er-Src	breast:	n/a	n/a
28	CTCF	chr1:120351483-120352179	A549	lung:	n/a	chr1:120351770-120351791 chr1:120351771-120351784 chr1:120351771-120351784 chr1:120351768-120351786 chr1:120351769-120351785
29	SRF	chr1:120351584-120352111	MCF-7	breast:	n/a	n/a
30	RCOR1	chr1:120351694-120352028	GM12878	blood:	n/a	n/a
31	RAD21	chr1:120351626-120351981	K562	blood:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
32	RAD21	chr1:120351515-120352120	Hela-S3	cervix:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
33	BHLHE40	chr1:120351727-120351977	GM12878	blood:	n/a	n/a
34	SRF	chr1:120351568-120352161	MCF-7	breast:	n/a	n/a
35	RAD21	chr1:120351593-120352059	H1-hESC	embryonic stem cell:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
36	CUX1	chr1:120351715-120352023	K562	blood:	n/a	n/a
37	RAD21	chr1:120351508-120352003	SK-N-SH_RA	brain:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
38	USF2	chr1:120351711-120352030	Hela-S3	cervix:	n/a	n/a
39	RAD21	chr1:120351482-120352050	HepG2	liver:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
40	RAD21	chr1:120351623-120352028	ECC-1	luminal epithelium:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
41	SMC3	chr1:120351099-120352106	SK-N-SH	brain:	n/a	chr1:120351770-120351784
42	E2F4	chr1:120351556-120352113	MCF10A-Er-Src	breast:	n/a	n/a
43	CTCF	chr1:120351625-120352039	HCT-116	colon:	n/a	chr1:120351770-120351791 chr1:120351771-120351784 chr1:120351771-120351784 chr1:120351768-120351786 chr1:120351769-120351785
44	MAFK	chr1:120351668-120352067	HepG2	liver:	n/a	n/a
45	TBL1XR1	chr1:120351502-120352021	K562	blood:	n/a	n/a
46	RAD21	chr1:120351566-120352064	A549	lung:	n/a	chr1:120351772-120351785 chr1:120351769-120351788 chr1:120351770-120351784 chr1:120351774-120351786
47	CTCF	chr1:120351465-120351998	GM12878	blood:	n/a	chr1:120351770-120351791 chr1:120351771-120351784 chr1:120351771-120351784 chr1:120351768-120351786 chr1:120351769-120351785
48	CTCF	chr1:120351523-120352015	IMR90	lung:	n/a	chr1:120351770-120351791 chr1:120351771-120351784 chr1:120351771-120351784 chr1:120351768-120351786 chr1:120351769-120351785
49	SMC3	chr1:120351572-120352006	Hela-S3	cervix:	n/a	chr1:120351770-120351784
50	MYC	chr1:120351526-120352113	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:120351585..120352102-chr7:123265949..123266449,2	MCF-7	breast:
2	chr1:120351445..120352265-chr1:120428419..120429413,4	MCF-7	breast:
3	chr1:120351738..120353782-chr1:120355581..120358346,2	K562	blood:
4	chr1:120350326..120353072-chr1:120353931..120356277,2	MCF-7	breast:

Variant related genes	Relation type
REG4	TF binding region
ENSG00000226446	Chromatin interaction
ENSG00000134193	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1815687	0.90[ASN][1000 genomes]
rs1856970	0.96[ASN][1000 genomes]
rs1856971	0.96[ASN][1000 genomes]
rs2153675	0.91[ASN][1000 genomes]
rs2153676	1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs2185608	0.91[ASN][1000 genomes]
rs2226084	0.90[ASN][1000 genomes]
rs2266023	0.82[ASN][1000 genomes]
rs2363611	0.90[ASN][1000 genomes]
rs2487572	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2487573	0.88[ASN][1000 genomes]
rs2495288	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs2793833	0.82[ASN][1000 genomes]
rs2793837	1.00[YRI][hapmap]
rs2843025	0.92[TSI][hapmap]
rs2994808	0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs2994810	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2994811	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2994812	0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2994813	0.93[ASN][1000 genomes]
rs2994814	0.96[ASN][1000 genomes]
rs2994815	0.90[ASN][1000 genomes]
rs2994816	0.90[ASN][1000 genomes]
rs2994817	0.90[ASN][1000 genomes]
rs2994818	0.90[ASN][1000 genomes]
rs2994819	0.90[ASN][1000 genomes]
rs2994820	0.87[ASN][1000 genomes]
rs2994821	0.85[ASN][1000 genomes]
rs2994822	0.83[ASN][1000 genomes]
rs3009182	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3009184	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs3009186	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs3009187	0.89[ASN][1000 genomes]
rs3009189	0.86[ASN][1000 genomes]
rs3009190	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3009192	0.87[ASN][1000 genomes]
rs3009194	0.90[ASN][1000 genomes]
rs3009195	0.96[ASN][1000 genomes]
rs3009196	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs3009197	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3009198	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs3009199	0.97[ASN][1000 genomes]
rs6697258	0.84[TSI][hapmap]
rs835565	0.88[ASN][1000 genomes]
rs835578	0.82[ASN][1000 genomes]
rs844346	0.82[ASN][1000 genomes]
rs856658	0.82[ASN][1000 genomes]
rs860674	0.98[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs947268	0.90[ASN][1000 genomes]
rs947274	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv915933	chr1:120323527-120471049	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv831226	chr1:120331599-120471049	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120349400-120355600	Enhancers	Liver	Liver
2	chr1:120349600-120354400	Weak transcription	HepG2	liver
3	chr1:120350800-120352000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:120350800-120352000	Enhancers	HSMM	muscle
5	chr1:120351200-120352000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:120351200-120352000	Enhancers	HMEC	breast
7	chr1:120351200-120352200	Enhancers	Dnd41	blood
8	chr1:120351400-120352000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:120351400-120352000	Enhancers	NHEK	skin
10	chr1:120351400-120352200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:120351600-120352400	Enhancers	Stomach Mucosa	stomach
12	chr1:120351600-120354000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:120351600-120357400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:120351800-120352000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:120351800-120352000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr1:120351800-120352000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:120351800-120352000	Enhancers	Duodenum Mucosa	Duodenum
18	chr1:120351800-120352000	Enhancers	Fetal Intestine Small	intestine
19	chr1:120351800-120352000	Enhancers	Fetal Kidney	kidney
20	chr1:120351800-120352000	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr1:120351800-120352200	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr1:120351800-120352200	Flanking Active TSS	Fetal Intestine Large	intestine
23	chr1:120351800-120357000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links