Variant report

Variant	rs1051997
Chromosome Location	chr7:112756994-112756995
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:112753755..112755851-chr7:112756779..112758396,2	MCF-7	breast:
2	chr7:112748491..112751404-chr7:112754696..112757418,3	MCF-7	breast:
3	chr7:112748064..112750116-chr7:112756047..112758575,2	MCF-7	breast:
4	chr7:112716768..112718529-chr7:112755627..112758248,2	K562	blood:
5	chr7:112089330..112091829-chr7:112756736..112758677,2	K562	blood:
6	chr7:112756695..112758581-chr7:112781055..112783118,2	K562	blood:
7	chr7:112747364..112749497-chr7:112755148..112758022,3	K562	blood:

Variant related genes	Relation type
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1008056	0.94[ASN][1000 genomes]
rs1013638	0.89[ASN][1000 genomes]
rs10228566	0.83[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10232914	0.91[ASN][1000 genomes]
rs10241909	0.91[ASN][1000 genomes]
rs10245805	0.91[ASN][1000 genomes]
rs10246011	0.87[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10246012	0.91[ASN][1000 genomes]
rs10252483	0.81[LWK][hapmap]
rs10257270	0.96[ASN][1000 genomes]
rs10267369	0.91[ASN][1000 genomes]
rs10269536	0.89[ASN][1000 genomes]
rs10278104	0.81[LWK][hapmap]
rs10278935	0.89[ASN][1000 genomes]
rs1051878	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1575013	0.95[CEU][hapmap];0.98[GIH][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1590155	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1807909	0.85[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2037657	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140913	0.85[CEU][hapmap]
rs2177800	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[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];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245834	0.89[CEU][hapmap]
rs2245985	0.85[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2246723	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2246724	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2246845	0.83[YRI][hapmap]
rs2249253	0.89[ASN][1000 genomes]
rs2249501	0.85[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2249511	0.91[ASN][1000 genomes]
rs2249612	0.85[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2250343	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2253640	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2253773	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2254842	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2264731	0.80[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2264732	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2462664	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2462665	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692601	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2699400	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28658090	0.91[ASN][1000 genomes]
rs55822923	0.96[ASN][1000 genomes]
rs55836916	0.91[ASN][1000 genomes]
rs56182321	0.89[ASN][1000 genomes]
rs56202345	0.89[ASN][1000 genomes]
rs56311133	0.91[ASN][1000 genomes]
rs56408134	0.91[ASN][1000 genomes]
rs73198873	0.91[ASN][1000 genomes]
rs73198882	0.91[ASN][1000 genomes]
rs7803528	0.81[ASN][1000 genomes]
rs9656199	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9656200	0.85[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758131	chr7:112492127-112768628	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759556	chr7:112492127-112768628	Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3355135	chr7:112616979-113134651	Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv435847	chr7:112618576-113134022	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3430638	chr7:112620663-113134403	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3442221	chr7:112620665-113134971	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv993501	chr7:112625029-113125338	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1022066	chr7:112630168-113122748	Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv539090	chr7:112630168-113122748	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv889059	chr7:112755548-112908788	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv970932	chr7:112756235-112757962	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1051997	GPR85	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112740600-112757600	Weak transcription	Right Atrium	heart
2	chr7:112740600-112758000	Weak transcription	Aorta	Aorta
3	chr7:112741000-112757600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr7:112743000-112757800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:112748800-112757600	Weak transcription	Colon Smooth Muscle	Colon
6	chr7:112748800-112757600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr7:112749000-112757400	Weak transcription	Left Ventricle	heart
8	chr7:112749200-112757400	Weak transcription	Psoas Muscle	Psoas
9	chr7:112749200-112757800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:112749600-112757400	Weak transcription	HMEC	breast
11	chr7:112749800-112757600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:112750000-112757400	Weak transcription	NHEK	skin
13	chr7:112750200-112757400	Weak transcription	NHLF	lung
14	chr7:112750400-112757200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr7:112750400-112757800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr7:112750600-112757400	Weak transcription	Osteobl	bone
17	chr7:112750800-112757800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:112750800-112757800	Weak transcription	Fetal Stomach	stomach
19	chr7:112751000-112757400	Weak transcription	HUVEC	blood vessel
20	chr7:112751000-112757400	Weak transcription	NHDF-Ad	bronchial
21	chr7:112751000-112758200	Weak transcription	Lung	lung
22	chr7:112751200-112757800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr7:112751200-112758200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr7:112751400-112757400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr7:112751400-112757600	Weak transcription	Primary T cells from cord blood	blood
26	chr7:112751600-112757400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:112751600-112757400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:112751600-112757600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr7:112751800-112757200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr7:112751800-112757400	Weak transcription	Brain Anterior Caudate	brain
31	chr7:112751800-112757400	Weak transcription	HSMMtube	muscle
32	chr7:112751800-112757800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr7:112751800-112757800	Weak transcription	Small Intestine	intestine
34	chr7:112752400-112757400	Weak transcription	Fetal Intestine Small	intestine
35	chr7:112752400-112757600	Weak transcription	Fetal Kidney	kidney
36	chr7:112752600-112757600	Weak transcription	Primary B cells from cord blood	blood
37	chr7:112752600-112757600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr7:112752600-112757800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr7:112752600-112757800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:112752600-112758600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr7:112752800-112757800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr7:112753000-112757800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr7:112753200-112757200	Strong transcription	K562	blood
44	chr7:112753200-112757800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr7:112753800-112757600	Weak transcription	Brain Germinal Matrix	brain
46	chr7:112754200-112757400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:112754200-112757400	Weak transcription	Right Ventricle	heart
48	chr7:112754200-112757400	Weak transcription	Spleen	Spleen
49	chr7:112754200-112757400	Weak transcription	GM12878-XiMat	blood
50	chr7:112754200-112757600	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links