Variant report

Variant	rs6694531
Chromosome Location	chr1:150683512-150683513
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150674686..150676800-chr1:150681691..150685110,3	K562	blood:
2	chr1:150681352..150684281-chr1:150686110..150688305,2	K562	blood:
3	chr1:150681352..150684293-chr1:150686425..150688305,2	K562	blood:

Variant related genes	Relation type
ENSG00000143452	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 38 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1053732	0.86[YRI][hapmap]
rs10888388	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204680	0.81[CHD][hapmap]
rs11204684	0.84[CHD][hapmap];0.80[GIH][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap]
rs11204693	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204695	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204702	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204712	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204725	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11204735	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11204737	0.89[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs1136774	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11800059	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12125650	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap]
rs12130363	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12403609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568757	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1971378	0.82[CHD][hapmap];0.80[GIH][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap]
rs2048558	0.81[CHD][hapmap]
rs34593358	0.85[AFR][1000 genomes]
rs486836	0.89[CEU][hapmap]
rs4970924	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970926	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];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587520	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66958685	0.85[AFR][1000 genomes]
rs7520022	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7534124	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9733	0.88[ASW][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv872417	chr1:150618632-150759979	Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv437158	chr1:150652202-150683512	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:38)

SNP	Gene	Cis/trans	Tissue	Source
rs6694531	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs6694531	CTSS	cis	multi-tissue	Pritchard
rs6694531	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs6694531	MCL1	cis	cerebellum	SCAN
rs6694531	CTSS	cis	parietal	SCAN
rs6694531	RP11-316M1.12	cis	Whole Blood	GTEx
rs6694531	CTSS	cis	cerebellum	SCAN
rs6694531	TXNIP	cis	parietal	SCAN
rs6694531	CTSK	cis	cerebellum	SCAN
rs6694531	CTSK	cis	multi-tissue	Pritchard
rs6694531	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs6694531	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs6694531	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs6694531	HORMAD1	cis	Esophagus Mucosa	GTEx
rs6694531	HORMAD1	cis	Nerve Tibial	GTEx
rs6694531	CTSS	cis	Nerve Tibial	GTEx
rs6694531	CTSK	cis	lymphoblastoid	seeQTL
rs6694531	ARNT	cis	normal skin	skin_eQTL
rs6694531	ARNT	cis	uninvolved skin	skin_eQTL
rs6694531	HORMAD1	cis	lesional skin	skin_eQTL
rs6694531	HORMAD1	cis	uninvolved skin	skin_eQTL
rs6694531	CTSK	cis	parietal	SCAN
rs6694531	HORMAD1	cis	normal skin	skin_eQTL
rs6694531	PSMD4	cis	parietal	SCAN
rs6694531	GOLPH3L	cis	Nerve Tibial	GTEx
rs6694531	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs6694531	HORMAD1	cis	parietal	SCAN
rs6694531	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs6694531	RP11-316M1.12	cis	Thyroid	GTEx
rs6694531	CTSS	cis	lymphoblastoid	seeQTL
rs6694531	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs6694531	ARNT	cis	cerebellum	SCAN
rs6694531	ARNT	cis	multi-tissue	Pritchard
rs6694531	ARNT	cis	Thyroid	GTEx
rs6694531	TCHHL1	cis	parietal	SCAN
rs6694531	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs6694531	ARNT	cis	parietal	SCAN
rs6694531	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150670600-150702600	Weak transcription	Hela-S3	cervix
2	chr1:150679200-150698600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr1:150681600-150702600	Weak transcription	A549	lung
4	chr1:150683200-150683800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr1:150683400-150683600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:150683400-150683600	Enhancers	K562	blood

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