Variant report

Variant	rs7520022
Chromosome Location	chr1:150659173-150659174
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150652709..150655600-chr1:150657493..150660351,2	MCF-7	breast:
2	chr1:150550587..150552161-chr1:150659135..150662073,2	MCF-7	breast:
3	chr1:150600872..150603791-chr1:150659144..150663270,3	MCF-7	breast:
4	chr1:150657524..150659198-chr1:150659977..150662845,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143384	Chromatin interaction
ENSG00000143420	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 32 )

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

rs_ID	r²[population]
rs1053732	0.86[YRI][hapmap]
rs10888388	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204680	0.81[CHD][hapmap]
rs11204684	0.83[CHD][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap]
rs11204693	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204695	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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204702	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204712	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204725	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[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]
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];0.88[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs1136774	0.83[AFR][1000 genomes]
rs11800059	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12125650	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap]
rs12130363	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12403609	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12568757	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1971378	0.81[CHD][hapmap];0.86[YRI][hapmap]
rs2048558	0.81[CHD][hapmap]
rs34593358	0.85[AFR][1000 genomes]
rs4970924	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970926	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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6587520	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6694531	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]
rs66958685	0.85[AFR][1000 genomes]
rs7534124	0.80[AFR][1000 genomes]
rs9733	0.88[ASW][hapmap];1.00[LWK][hapmap];0.90[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	nsv1014638	chr1:150647987-150679033	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:32)

SNP	Gene	Cis/trans	Tissue	Source
rs7520022	TXNIP	cis	parietal	SCAN
rs7520022	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs7520022	RP11-316M1.12	cis	Thyroid	GTEx
rs7520022	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs7520022	CTSS	cis	Nerve Tibial	GTEx
rs7520022	CTSS	cis	cerebellum	SCAN
rs7520022	ARNT	cis	parietal	SCAN
rs7520022	PSMD4	cis	parietal	SCAN
rs7520022	CTSK	cis	multi-tissue	Pritchard
rs7520022	HORMAD1	cis	Esophagus Mucosa	GTEx
rs7520022	GOLPH3L	cis	Nerve Tibial	GTEx
rs7520022	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs7520022	HORMAD1	cis	Nerve Tibial	GTEx
rs7520022	CTSS	cis	parietal	SCAN
rs7520022	CTSK	cis	lymphoblastoid	seeQTL
rs7520022	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs7520022	CTSS	cis	lymphoblastoid	seeQTL
rs7520022	CTSS	cis	multi-tissue	Pritchard
rs7520022	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs7520022	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs7520022	CTSK	cis	parietal	SCAN
rs7520022	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs7520022	CTSK	cis	cerebellum	SCAN
rs7520022	TCHHL1	cis	parietal	SCAN
rs7520022	HORMAD1	cis	parietal	SCAN
rs7520022	MCL1	cis	cerebellum	SCAN
rs7520022	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs7520022	RP11-316M1.12	cis	Whole Blood	GTEx
rs7520022	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs7520022	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs7520022	ARNT	cis	Thyroid	GTEx
rs7520022	ARNT	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150603200-150661200	Weak transcription	Brain Substantia Nigra	brain
2	chr1:150603400-150668200	Weak transcription	Brain Germinal Matrix	brain
3	chr1:150608600-150668600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:150618800-150660400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:150621000-150660800	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:150621200-150660400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:150621200-150664800	Weak transcription	Fetal Brain Female	brain
8	chr1:150621200-150665000	Weak transcription	Fetal Kidney	kidney
9	chr1:150621200-150669400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:150621400-150660400	Weak transcription	HSMM	muscle
11	chr1:150621800-150661200	Weak transcription	NHDF-Ad	bronchial
12	chr1:150621800-150668600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:150622000-150661400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:150622000-150668600	Weak transcription	HSMMtube	muscle
15	chr1:150622000-150669400	Weak transcription	Esophagus	oesophagus
16	chr1:150622200-150660600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:150623200-150668600	Weak transcription	Brain Angular Gyrus	brain
18	chr1:150623400-150663000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:150630000-150664800	Weak transcription	Thymus	Thymus
20	chr1:150631800-150665400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:150632400-150669000	Weak transcription	Aorta	Aorta
22	chr1:150632600-150665000	Weak transcription	Colonic Mucosa	Colon
23	chr1:150632600-150668200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:150633000-150668600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:150633200-150669200	Weak transcription	Left Ventricle	heart
26	chr1:150633400-150660600	Weak transcription	Fetal Lung	lung
27	chr1:150633400-150665000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:150634600-150660400	Weak transcription	K562	blood
29	chr1:150634600-150660800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:150634600-150661200	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr1:150634600-150664800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:150634800-150660000	Weak transcription	NHEK	skin
33	chr1:150635400-150660400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:150636200-150660600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:150636400-150661800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:150636400-150666600	Weak transcription	Brain Anterior Caudate	brain
37	chr1:150640000-150661200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:150640000-150663800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:150640400-150667600	Weak transcription	Pancreas	Pancrea
40	chr1:150641000-150661200	Weak transcription	Hela-S3	cervix
41	chr1:150641200-150669400	Weak transcription	Gastric	stomach
42	chr1:150642000-150663000	Weak transcription	A549	lung
43	chr1:150643400-150666800	Strong transcription	Fetal Intestine Small	intestine
44	chr1:150644200-150659600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:150648000-150660600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:150648800-150664800	Weak transcription	Lung	lung
47	chr1:150648800-150669400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:150648800-150669400	Weak transcription	Spleen	Spleen
49	chr1:150652400-150662200	Weak transcription	Psoas Muscle	Psoas
50	chr1:150654400-150661400	Weak transcription	Osteobl	bone

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