Variant report

Variant	rs3815878
Chromosome Location	chr2:182761117-182761118
allele	G/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	chr2:182760384-182761573	MCF10A-Er-Src	breast:	n/a	n/a
2	HNF4G	chr2:182761053-182761373	HepG2	liver:	n/a	chr2:182761205-182761219 chr2:182761205-182761220 chr2:182761198-182761213 chr2:182761203-182761221 chr2:182761203-182761218 chr2:182761198-182761213 chr2:182761205-182761220 chr2:182761206-182761219 chr2:182761205-182761218 chr2:182761205-182761220 chr2:182761198-182761212 chr2:182761206-182761218 chr2:182761198-182761211 chr2:182761205-182761220 chr2:182761198-182761211
3	HNF4A	chr2:182761031-182761426	HepG2	liver:	n/a	chr2:182761205-182761219 chr2:182761205-182761220 chr2:182761198-182761213 chr2:182761203-182761221 chr2:182761198-182761213 chr2:182761205-182761220 chr2:182761206-182761219 chr2:182761204-182761219 chr2:182761205-182761218 chr2:182761205-182761220 chr2:182761198-182761212 chr2:182761206-182761218 chr2:182761198-182761211 chr2:182761205-182761220 chr2:182761198-182761211
4	FOXA1	chr2:182760899-182761394	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:182761094-182762113	Hela-S3	cervix:	n/a	n/a
6	FOXA1	chr2:182761060-182761333	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:182759864-182762129	MCF-7	breast:	n/a	n/a
8	POLR2A	chr2:182759737-182762987	K562	blood:	n/a	n/a
9	FOXA2	chr2:182761058-182761310	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:182755351-182762286	Hela-S3	cervix:	n/a	n/a
11	HNF4A	chr2:182760993-182761377	HepG2	liver:	n/a	chr2:182761205-182761219 chr2:182761205-182761220 chr2:182761198-182761213 chr2:182761203-182761221 chr2:182761198-182761213 chr2:182761205-182761220 chr2:182761206-182761219 chr2:182761204-182761219 chr2:182761205-182761218 chr2:182761205-182761220 chr2:182761198-182761212 chr2:182761206-182761218 chr2:182761198-182761211 chr2:182761205-182761220 chr2:182761198-182761211
12	POLR2A	chr2:182760099-182762213	HCT-116	colon:	n/a	n/a
13	HDAC2	chr2:182761076-182761379	HepG2	liver:	n/a	n/a
14	POLR2A	chr2:182760174-182761989	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:182757398..182762251-chr2:182784880..182789284,4	K562	blood:
2	chr2:182759840..182761573-chr2:182989686..182991505,2	MCF-7	breast:
3	chr2:182615557..182618410-chr2:182759397..182761263,2	MCF-7	breast:
4	chr2:182659802..182662232-chr2:182760144..182763028,2	MCF-7	breast:
5	chr2:182760700..182762918-chr2:182812910..182815016,2	MCF-7	breast:
6	chr2:182760625..182763204-chr2:182996847..182998737,3	MCF-7	breast:
7	chr2:182753988..182769660-chr2:182938612..182954194,58	MCF-7	breast:
8	chr2:182601328..182613741-chr2:182753153..182773539,79	MCF-7	breast:
9	chr2:182759435..182761686-chr2:182994619..182996651,2	MCF-7	breast:
10	chr11:65189514..65192063-chr2:182759312..182761932,2	MCF-7	breast:
11	chr2:182601728..182612786-chr2:182754371..182769481,60	MCF-7	breast:

Variant related genes	Relation type
SSFA2	TF binding region
ENSG00000260742	TF binding region
ENSG00000245532	Chromatin interaction
ENSG00000221023	Chromatin interaction
ENSG00000265129	Chromatin interaction
ENSG00000138434	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10165936	1.00[CEU][hapmap]
rs10166975	0.80[EUR][1000 genomes]
rs10173114	1.00[CEU][hapmap]
rs10176061	1.00[CEU][hapmap]
rs10176613	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs10176757	1.00[CEU][hapmap]
rs10179363	1.00[CEU][hapmap]
rs10179547	1.00[CEU][hapmap]
rs10189187	0.84[EUR][1000 genomes]
rs10191082	0.80[EUR][1000 genomes]
rs10197254	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10199645	1.00[CEU][hapmap]
rs10200243	1.00[CEU][hapmap]
rs10201303	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10210215	1.00[CEU][hapmap]
rs10221891	1.00[CEU][hapmap]
rs13389121	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13401364	0.84[EUR][1000 genomes]
rs13404156	1.00[CEU][hapmap]
rs13425734	1.00[CEU][hapmap]
rs1528024	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1528025	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1528026	0.80[EUR][1000 genomes]
rs1528027	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs16867498	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs16867509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17456384	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881158	1.00[CEU][hapmap]
rs1881159	1.00[CEU][hapmap]
rs2059702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2368224	1.00[CEU][hapmap]
rs2368235	0.84[EUR][1000 genomes]
rs3731693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4597477	0.80[EUR][1000 genomes]
rs55732891	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55758877	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433943	1.00[CEU][hapmap]
rs6707164	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6707654	0.80[EUR][1000 genomes]
rs6720109	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6720702	1.00[CEU][hapmap]
rs6723011	0.80[EUR][1000 genomes]
rs6735322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6736341	0.80[EUR][1000 genomes]
rs6736766	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6739707	0.80[EUR][1000 genomes]
rs6744556	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748354	1.00[CEU][hapmap]
rs6751464	0.80[EUR][1000 genomes]
rs6751685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754819	0.80[EUR][1000 genomes]
rs6755017	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73032623	0.84[EUR][1000 genomes]
rs7557969	1.00[CEU][hapmap]
rs7562680	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs7563333	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7580410	1.00[CEU][hapmap]
rs7603721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606321	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7608942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9807949	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs9808112	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv834478	chr2:182654811-182843201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv834479	chr2:182738483-182905444	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182756000-182762200	Active TSS	Colonic Mucosa	Colon
2	chr2:182757200-182762000	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr2:182757600-182764200	Weak transcription	Gastric	stomach
4	chr2:182757600-182764200	Weak transcription	Spleen	Spleen
5	chr2:182757800-182761600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:182757800-182763800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr2:182757800-182764000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:182757800-182764200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:182757800-182764200	Weak transcription	Pancreas	Pancrea
10	chr2:182757800-182766400	Weak transcription	Lung	lung
11	chr2:182757800-182779400	Weak transcription	Esophagus	oesophagus
12	chr2:182757800-182779800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:182757800-182790400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:182758000-182764000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr2:182758000-182764000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:182758000-182765800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:182758000-182780000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:182758000-182783200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr2:182758200-182764800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:182758200-182779800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:182758200-182780200	Weak transcription	Brain Germinal Matrix	brain
22	chr2:182758400-182764200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:182758400-182764200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:182758400-182766800	Weak transcription	Fetal Brain Female	brain
25	chr2:182758800-182761200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
26	chr2:182759000-182764200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:182759000-182764400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:182759200-182761400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr2:182759200-182762800	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr2:182759200-182763200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr2:182759200-182763600	Weak transcription	Primary B cells from cord blood	blood
32	chr2:182759200-182763800	Weak transcription	Fetal Brain Male	brain
33	chr2:182759200-182763800	Weak transcription	Fetal Muscle Leg	muscle
34	chr2:182759200-182763800	Weak transcription	Ovary	ovary
35	chr2:182759200-182764000	Enhancers	Brain Substantia Nigra	brain
36	chr2:182759200-182764000	Weak transcription	Left Ventricle	heart
37	chr2:182759200-182766000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:182759200-182783800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr2:182759400-182761400	Weak transcription	Placenta	Placenta
40	chr2:182759400-182761600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:182759400-182762000	Enhancers	Fetal Heart	heart
42	chr2:182759400-182763400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:182759400-182763400	Weak transcription	Stomach Mucosa	stomach
44	chr2:182759400-182763600	Weak transcription	HSMMtube	muscle
45	chr2:182759400-182763800	Weak transcription	Primary T cells from cord blood	blood
46	chr2:182759400-182764000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:182759400-182764400	Weak transcription	Thymus	Thymus
48	chr2:182759400-182764800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr2:182759600-182762000	Genic enhancers	Monocytes-CD14+_RO01746	blood
50	chr2:182759600-182762800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links