Variant report

Variant	rs7608942
Chromosome Location	chr2:182820101-182820102
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:182820077..182822937-chr2:182942227..182944128,2	MCF-7	breast:
2	chr2:182755199..182758124-chr2:182816359..182820685,4	MCF-7	breast:
3	chr2:182819036..182820920-chr2:182951975..182953490,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260742	Chromatin interaction
ENSG00000265129	Chromatin interaction
ENSG00000138434	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10165936	1.00[CEU][hapmap]
rs10173114	1.00[CEU][hapmap]
rs10176061	1.00[CEU][hapmap]
rs10176613	1.00[CEU][hapmap]
rs10176757	1.00[CEU][hapmap]
rs10179363	1.00[CEU][hapmap]
rs10179547	1.00[CEU][hapmap]
rs10199645	1.00[CEU][hapmap]
rs10200243	1.00[CEU][hapmap]
rs10201303	1.00[CEU][hapmap]
rs10210215	1.00[CEU][hapmap]
rs10221891	1.00[CEU][hapmap]
rs13389121	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13404156	1.00[CEU][hapmap]
rs13425734	1.00[CEU][hapmap]
rs1528024	1.00[CEU][hapmap]
rs1528025	1.00[CEU][hapmap]
rs1528027	1.00[CEU][hapmap]
rs16867498	1.00[CEU][hapmap]
rs16867509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17456384	0.87[EUR][1000 genomes];0.88[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];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2288330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2303554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2368224	1.00[CEU][hapmap]
rs3731693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3815877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3815878	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]
rs55732891	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55758877	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433943	1.00[CEU][hapmap]
rs6707164	1.00[CEU][hapmap]
rs6720109	1.00[CEU][hapmap]
rs6720702	1.00[CEU][hapmap]
rs6735322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6736766	1.00[CEU][hapmap]
rs6744556	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6748354	1.00[CEU][hapmap]
rs6751685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6754192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6755017	1.00[CEU][hapmap];0.86[GIH][hapmap];0.84[EUR][1000 genomes]
rs7557969	1.00[CEU][hapmap]
rs7562680	1.00[CEU][hapmap]
rs7563333	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7580410	1.00[CEU][hapmap]
rs7603721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7606321	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9807949	1.00[CEU][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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7608942	EGR2	trans	brain	seeQTL
rs7608942	GPR3	trans	brain	seeQTL
rs7608942	ADAD2	trans	brain	seeQTL
rs7608942	NPAS4	trans	brain	seeQTL
rs7608942	PTGS2	trans	brain	seeQTL
rs7608942	EGR1	trans	brain	seeQTL
rs7608942	INHBA	trans	brain	seeQTL
rs7608942	LBH	trans	brain	seeQTL
rs7608942	SLC2A3	trans	brain	seeQTL
rs7608942	CCL4	trans	brain	seeQTL
rs7608942	FOSB	trans	brain	seeQTL
rs7608942	EGR4	trans	brain	seeQTL
rs7608942	CCL3	trans	brain	seeQTL
rs7608942	DUSP2	trans	brain	seeQTL
rs7608942	ARC	trans	brain	seeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182815600-182820600	Enhancers	Hela-S3	cervix
2	chr2:182818000-182820400	Enhancers	Placenta Amnion	Placenta Amnion
3	chr2:182818600-182820400	Flanking Active TSS	Dnd41	blood
4	chr2:182818600-182820400	Enhancers	HMEC	breast
5	chr2:182818800-182820400	Enhancers	Stomach Mucosa	stomach
6	chr2:182818800-182820400	Active TSS	Thymus	Thymus
7	chr2:182819200-182820200	Enhancers	HSMM	muscle
8	chr2:182819200-182820400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:182819200-182822400	Weak transcription	Pancreas	Pancrea
10	chr2:182819200-182822600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:182819200-182822600	Weak transcription	Fetal Intestine Small	intestine
12	chr2:182819200-182828200	Weak transcription	Right Atrium	heart
13	chr2:182819400-182820200	Flanking Active TSS	Liver	Liver
14	chr2:182819400-182820400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:182819400-182820400	Enhancers	Osteobl	bone
16	chr2:182819400-182820600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:182819400-182822400	Weak transcription	Fetal Intestine Large	intestine
18	chr2:182819400-182822800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:182819400-182823000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:182819600-182820200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:182819600-182820200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:182819600-182820400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:182819600-182820600	Enhancers	NHDF-Ad	bronchial
24	chr2:182819600-182825800	Weak transcription	Fetal Heart	heart
25	chr2:182819800-182820200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:182819800-182820200	Enhancers	A549	lung
27	chr2:182819800-182820400	Enhancers	Primary T cells from cord blood	blood
28	chr2:182819800-182820400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:182819800-182820400	Enhancers	NH-A	brain
30	chr2:182819800-182820600	Enhancers	Muscle Satellite Cultured Cells	--
31	chr2:182819800-182820600	Active TSS	Fetal Thymus	thymus
32	chr2:182819800-182820600	Enhancers	HUVEC	blood vessel
33	chr2:182819800-182822400	Weak transcription	Small Intestine	intestine
34	chr2:182819800-182822800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:182819800-182822800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:182819800-182825200	Weak transcription	Fetal Stomach	stomach
37	chr2:182820000-182820200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:182820000-182820400	Flanking Active TSS	NHEK	skin
39	chr2:182820000-182822000	Weak transcription	HepG2	liver
40	chr2:182820000-182822400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:182820000-182822400	Weak transcription	NHLF	lung

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