Variant report

Variant	rs9530
Chromosome Location	chr7:65425894-65425895
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65420692..65422750-chr7:65424011..65425945,2	MCF-7	breast:
2	chr18:9614542..9615101-chr7:65425383..65426101,2	Hela-S3	cervix:
3	chr7:65425587..65427267-chr7:65432943..65434454,2	K562	blood:

Variant related genes	Relation type
ENSG00000154845	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10229450	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10279841	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10807697	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1167384	0.81[EUR][1000 genomes]
rs1167385	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1167386	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11763147	0.96[CEU][hapmap];0.93[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.93[LWK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap]
rs11768292	0.83[EUR][1000 genomes]
rs11770828	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs12670952	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12698512	0.81[EUR][1000 genomes]
rs13237956	0.82[EUR][1000 genomes]
rs1631091	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1701751	0.90[EUR][1000 genomes]
rs1701757	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1701760	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1723268	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1723275	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1829943	0.95[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap]
rs1880556	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1917563	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2008188	0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2462573	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2658585	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2658587	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2690442	0.96[CEU][hapmap];0.93[CHB][hapmap]
rs2692056	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2939548	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2946579	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2949690	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2949692	0.91[EUR][1000 genomes]
rs3201569	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34973832	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35135885	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35850374	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4467826	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4718288	0.81[EUR][1000 genomes]
rs55773927	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55796207	0.82[EUR][1000 genomes]
rs56028712	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62470893	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66552782	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6945322	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6954920	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6955582	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6960048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs709604	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs736270	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7383796	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7784623	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7791814	0.96[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7809991	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs781143	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs781144	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs781145	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs781151	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs781152	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1020337	chr7:65371505-65449654	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
4	nsv1025494	chr7:65402301-65515606	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv538906	chr7:65402301-65515606	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv888321	chr7:65408904-65449541	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	esv9823	chr7:65413362-65468020	Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	esv3426468	chr7:65413488-65462982	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	esv3433491	chr7:65414034-65463477	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	nsv1028971	chr7:65414064-65457437	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
11	nsv966831	chr7:65415065-65428348	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv888322	chr7:65415647-65466565	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	nsv538907	chr7:65417400-65456089	Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
14	nsv888323	chr7:65418355-65461080	ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
15	nsv888324	chr7:65418876-65466565	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs9530	ERV3	cis	cerebellum	SCAN
rs9530	KCTD7	cis	parietal	SCAN
rs9530	GUSB	cis	parietal	SCAN
rs9530	RP4-756H11.3	cis	Thyroid	GTEx
rs9530	RP4-756H11.3	cis	Artery Tibial	GTEx
rs9530	GUSB	cis	cerebellum	SCAN
rs9530	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs9530	RABGEF1	cis	cerebellum	SCAN
rs9530	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs9530	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs9530	RP4-756H11.3	cis	Artery Aorta	GTEx
rs9530	CRCP	cis	parietal	SCAN
rs9530	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs9530	RP4-756H11.3	cis	lung	GTEx
rs9530	ZNF273	cis	cerebellum	SCAN
rs9530	CRCP	cis	cerebellum	SCAN
rs9530	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs9530	ERV3	cis	parietal	SCAN
rs9530	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs9530	RP4-756H11.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65412200-65428200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr7:65417800-65432400	Weak transcription	Stomach Mucosa	stomach
3	chr7:65417800-65441600	Strong transcription	Primary T cells from cord blood	blood
4	chr7:65417800-65445400	Weak transcription	Fetal Heart	heart
5	chr7:65418000-65445400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr7:65418200-65434400	Strong transcription	A549	lung
7	chr7:65418400-65442400	Strong transcription	Adipose Nuclei	Adipose
8	chr7:65418400-65445200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:65418800-65427200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr7:65418800-65442400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:65418800-65444000	Strong transcription	Dnd41	blood
12	chr7:65418800-65445200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:65418800-65445400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:65418800-65445600	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr7:65418800-65446000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr7:65419000-65440200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:65419000-65440600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr7:65419000-65442400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr7:65419000-65442400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr7:65419000-65442600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr7:65419000-65445200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr7:65419000-65445400	Strong transcription	Fetal Thymus	thymus
23	chr7:65419000-65445400	Strong transcription	Thymus	Thymus
24	chr7:65419200-65445200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:65419400-65445200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr7:65419600-65426000	Strong transcription	GM12878-XiMat	blood
27	chr7:65419600-65442400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr7:65419600-65444800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr7:65419800-65445400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:65420200-65445200	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr7:65420400-65442200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr7:65420600-65442400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr7:65420600-65442400	Strong transcription	Fetal Brain Female	brain
34	chr7:65421600-65428200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr7:65422400-65444800	Strong transcription	Brain Germinal Matrix	brain
36	chr7:65422400-65445600	Weak transcription	Right Atrium	heart
37	chr7:65422600-65442400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr7:65422800-65440600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:65423000-65426000	Strong transcription	NH-A	brain
40	chr7:65423000-65426200	Strong transcription	Primary hematopoietic stem cells	blood
41	chr7:65423000-65433000	Strong transcription	Primary B cells from cord blood	blood
42	chr7:65423000-65441200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr7:65423000-65441200	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr7:65423000-65442400	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr7:65423000-65442400	Strong transcription	Stomach Smooth Muscle	stomach
46	chr7:65423000-65444800	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr7:65423000-65445600	Strong transcription	Fetal Intestine Large	intestine
48	chr7:65423200-65426200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr7:65423200-65426600	Strong transcription	HUVEC	blood vessel
50	chr7:65423200-65442400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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