Variant report

Variant	rs2161312
Chromosome Location	chr5:95184220-95184221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:94984590..94987808-chr5:95181177..95184579,4	K562	blood:
2	chr5:95066232..95068400-chr5:95182417..95184649,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164292	Chromatin interaction
ENSG00000250240	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10044151	1.00[CHB][hapmap]
rs10055875	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10067941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10079710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12520664	1.00[ASN][1000 genomes]
rs2546196	1.00[ASN][1000 genomes]
rs3797207	0.88[CEU][hapmap];0.88[CHD][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs41470049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6420125	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6556887	0.91[ASN][1000 genomes]
rs6556888	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6882301	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6883552	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6884979	0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7702848	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7703084	0.91[ASN][1000 genomes]
rs7708375	1.00[ASN][1000 genomes]
rs7716279	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7719227	1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2161312	CHD1	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95171800-95185800	Weak transcription	Pancreas	Pancrea
2	chr5:95177800-95192200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:95178400-95188400	Weak transcription	Stomach Mucosa	stomach
4	chr5:95179000-95186200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:95179000-95206000	Weak transcription	Spleen	Spleen
6	chr5:95179200-95185800	Weak transcription	Lung	lung
7	chr5:95179400-95184600	Weak transcription	NH-A	brain
8	chr5:95179400-95184600	Weak transcription	NHDF-Ad	bronchial
9	chr5:95179600-95184400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:95179800-95185200	Weak transcription	Left Ventricle	heart
11	chr5:95180000-95186000	Weak transcription	Right Atrium	heart
12	chr5:95180200-95184600	Weak transcription	Adipose Nuclei	Adipose
13	chr5:95182000-95185200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr5:95182600-95186200	Weak transcription	NHLF	lung
15	chr5:95182800-95184400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:95182800-95184400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:95182800-95185800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:95182800-95185800	Weak transcription	Placenta	Placenta
19	chr5:95182800-95185800	Weak transcription	HepG2	liver
20	chr5:95182800-95186000	Enhancers	Liver	Liver
21	chr5:95182800-95191000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr5:95182800-95191000	Weak transcription	Brain Substantia Nigra	brain
23	chr5:95182800-95191200	Weak transcription	Psoas Muscle	Psoas
24	chr5:95182800-95191800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr5:95182800-95192200	Weak transcription	Esophagus	oesophagus
26	chr5:95183000-95184400	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr5:95183000-95185000	Enhancers	Fetal Heart	heart
28	chr5:95183400-95186000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr5:95183600-95186600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:95183600-95186800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr5:95183800-95185200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:95184200-95185000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr5:95184200-95185000	Enhancers	HSMM	muscle
34	chr5:95184200-95185000	Enhancers	Osteobl	bone
35	chr5:95184200-95186600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links