Variant report

Variant	rs287980
Chromosome Location	chr2:9971366-9971367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9939277..9941879-chr2:9968461..9972329,3	K562	blood:
2	chr2:9971098..9974311-chr2:9982835..9984808,3	K562	blood:
3	chr2:9969831..9974999-chr2:9980864..9985156,9	MCF-7	breast:
4	chr2:9954341..9956671-chr2:9971127..9973681,2	K562	blood:
5	chr2:9968571..9971604-chr2:9981989..9985687,7	MCF-7	breast:
6	chr2:9970684..9971435-chr2:9983705..9984702,2	MCF-7	breast:
7	chr2:9952588..9955831-chr2:9967859..9972229,5	MCF-7	breast:
8	chr2:9970023..9972600-chr2:9978871..9981245,2	K562	blood:

Variant related genes	Relation type
ENSG00000115750	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1119632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1119633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887231	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429581	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867192	0.88[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs16867203	0.89[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs2656329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287975	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287976	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287978	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287982	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2884174	0.83[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs56154233	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57352580	0.87[ASN][1000 genomes]
rs58521916	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72780999	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72782605	0.91[ASN][1000 genomes]
rs72782633	0.87[ASN][1000 genomes]
rs72782634	0.88[ASN][1000 genomes]
rs72782637	0.88[ASN][1000 genomes]
rs9973577	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973654	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973905	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv528645	chr2:9946213-9975557	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	nsv873622	chr2:9948404-9971366	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv873624	chr2:9949464-9971366	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv873625	chr2:9949464-9971366	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv469416	chr2:9949464-9975557	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
10	nsv873626	chr2:9949464-9975557	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
11	nsv873627	chr2:9949464-9982608	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
12	nsv873628	chr2:9949464-9985670	Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
13	nsv873629	chr2:9949464-10016627	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
14	nsv469427	chr2:9951970-9975557	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
15	nsv580959	chr2:9951970-9975557	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
16	nsv873630	chr2:9953949-10030024	Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs287980	TAF1B	cis	lymphoblastoid	seeQTL
rs287980	TAF1B	Cis_1M	lymphoblastoid	RTeQTL
rs287980	TAF1B	cis	cerebellum	SCAN
rs287980	CMPK2	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9955200-9983000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:9960800-9971800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:9970000-9972000	Enhancers	Stomach Mucosa	stomach
4	chr2:9970200-9971800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:9970200-9972000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:9970200-9972400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:9970600-9971400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:9970600-9973000	Enhancers	HMEC	breast
9	chr2:9970800-9971400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:9970800-9971400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
11	chr2:9970800-9971400	Flanking Active TSS	NHEK	skin
12	chr2:9970800-9971600	Enhancers	Fetal Kidney	kidney
13	chr2:9970800-9972000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr2:9970800-9972200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:9970800-9973400	Enhancers	Placenta	Placenta
16	chr2:9970800-9973600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:9971000-9971400	Enhancers	Pancreas	Pancrea
18	chr2:9971000-9971600	Enhancers	Hela-S3	cervix
19	chr2:9971000-9971600	Enhancers	NHDF-Ad	bronchial
20	chr2:9971000-9972200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr2:9971000-9972200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:9971000-9972200	Enhancers	K562	blood
23	chr2:9971200-9971400	Enhancers	Brain Germinal Matrix	brain
24	chr2:9971200-9971400	Enhancers	Duodenum Mucosa	Duodenum
25	chr2:9971200-9971400	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr2:9971200-9972200	Bivalent Enhancer	Fetal Lung	lung
27	chr2:9971200-9972600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:9971200-9972600	Enhancers	Esophagus	oesophagus
29	chr2:9971200-9972800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:9971200-9973000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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