Variant report

Variant	rs705866
Chromosome Location	chr7:99965285-99965286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99955250..99958076-chr7:99963058..99965429,2	K562	blood:
2	chr7:99964978..99968212-chr7:99999516..100003937,4	K562	blood:
3	chr7:99953918..99957943-chr7:99965213..99968518,4	K562	blood:
4	chr7:99964487..99968212-chr7:99999516..100003937,5	K562	blood:
5	chr7:99953591..99956597-chr7:99962899..99966077,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PILRB-1	chr7:99964972-99965451	NONHSAT122358

Variant related genes	Relation type
ENSG00000078487	Chromatin interaction
ENSG00000121716	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 59 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1000215	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10085549	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10241492	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs1059129	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1063945	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1073	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs11559117	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs11760536	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap]
rs11761253	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761306	1.00[ASN][1000 genomes]
rs11761426	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761725	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap]
rs11761784	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs11763414	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11763511	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs11765869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766752	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs11766917	0.83[ASN][1000 genomes]
rs11768933	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768967	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769057	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769700	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs11769886	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.84[ASN][1000 genomes]
rs11771241	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11771419	0.84[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771799	1.00[ASN][1000 genomes]
rs11771936	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11773661	0.85[CEU][hapmap]
rs1636980	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1962269	0.91[CEU][hapmap]
rs1964242	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003507	0.84[ASN][1000 genomes]
rs2108269	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406253	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs2406255	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap]
rs28401739	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28490152	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs28495773	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28578163	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs28660238	0.84[ASN][1000 genomes]
rs28680963	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087502	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34989573	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs35111986	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.84[ASN][1000 genomes]
rs35986051	1.00[ASN][1000 genomes]
rs3900792	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3991498	0.84[EUR][1000 genomes]
rs3991564	0.93[EUR][1000 genomes]
rs4074838	0.83[CHD][hapmap];1.00[GIH][hapmap]
rs41280971	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4472444	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs61735533	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66632384	0.84[ASN][1000 genomes]
rs67163493	0.84[ASN][1000 genomes]
rs67315960	0.84[ASN][1000 genomes]
rs67471932	0.84[ASN][1000 genomes]
rs68116612	0.84[ASN][1000 genomes]
rs6945952	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6946768	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948685	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953749	0.84[ASN][1000 genomes]
rs6955362	0.85[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap]
rs6955367	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957928	0.84[ASN][1000 genomes]
rs6965207	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965458	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970806	0.84[ASN][1000 genomes]
rs6975514	0.85[CEU][hapmap]
rs6975563	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975660	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975729	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs6979910	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73161745	0.85[ASN][1000 genomes]
rs73161759	0.84[ASN][1000 genomes]
rs73161762	0.84[ASN][1000 genomes]
rs73401443	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401450	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73401451	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7341507	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7783159	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.84[ASN][1000 genomes]
rs7783550	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7786844	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787620	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs7792525	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792959	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7794485	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[MKK][hapmap]
rs7795656	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7795805	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799894	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799901	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7799932	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803454	0.84[ASN][1000 genomes]
rs7809801	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
2	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
3	nsv831071	chr7:99918025-100113413	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	287 gene(s)	inside rSNPs	diseases

mRNA abundance (count:59)

SNP	Gene	Cis/trans	Tissue	Source
rs705866	GNB2	cis	parietal	SCAN
rs705866	GATS	cis	parietal	SCAN
rs705866	PILRA	cis	Adipose Subcutaneous	GTEx
rs705866	PILRB	cis	Nerve Tibial	GTEx
rs705866	PILRB	cis	Heart Left Ventricle	GTEx
rs705866	STAG3L5P	cis	Thyroid	GTEx
rs705866	PILRB	cis	Artery Tibial	GTEx
rs705866	ZCWPW1	cis	cerebellum	SCAN
rs705866	PILRB	cis	Thyroid	GTEx
rs705866	PILRA	cis	Nerve Tibial	GTEx
rs705866	PILRB	cis	Skin Sun Exposed Lower leg	GTEx
rs705866	PILRA	cis	parietal	SCAN
rs705866	PVRIG2P	cis	Nerve Tibial	GTEx
rs705866	STAG3L5P	cis	Esophagus Muscularis	GTEx
rs705866	PVRIG2P	cis	Esophagus Mucosa	GTEx
rs705866	STAG3L5P	cis	Artery Tibial	GTEx
rs705866	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs705866	STAG3L5P	cis	Nerve Tibial	GTEx
rs705866	STAG3L5P	cis	Muscle Skeletal	GTEx
rs705866	PILRB	cis	parietal	SCAN
rs705866	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs705866	PILRA	cis	Thyroid	GTEx
rs705866	PVRIG2P	cis	Heart Left Ventricle	GTEx
rs705866	CNPY4	cis	cerebellum	SCAN
rs705866	PILRB	cis	lung	GTEx
rs705866	STAG3L5P	cis	Adipose Subcutaneous	GTEx
rs705866	PILRA	cis	Esophagus Mucosa	GTEx
rs705866	PILRA	cis	Stomach	GTEx
rs705866	PILRB	cis	lymphoblastoid	seeQTL
rs705866	PILRA	cis	Muscle Skeletal	GTEx
rs705866	STAG3L5P	cis	Skin Sun Exposed Lower leg	GTEx
rs705866	PILRA	cis	Esophagus Muscularis	GTEx
rs705866	STAG3L5P	cis	lung	GTEx
rs705866	ORAI2	cis	cerebellum	SCAN
rs705866	STAG3L5P	cis	Artery Aorta	GTEx
rs705866	STAG3L5P	cis	Esophagus Mucosa	GTEx
rs705866	PVRIG2P	cis	Artery Tibial	GTEx
rs705866	PILRA	cis	Artery Tibial	GTEx
rs705866	PILRB	cis	Esophagus Muscularis	GTEx
rs705866	ZCWPW1	cis	parietal	SCAN
rs705866	STAG3	cis	lymphoblastoid	seeQTL
rs705866	PILRB	cis	Esophagus Mucosa	GTEx
rs705866	PILRA	cis	Artery Aorta	GTEx
rs705866	PILRB	cis	Artery Aorta	GTEx
rs705866	PILRA	cis	Heart Left Ventricle	GTEx
rs705866	PVRIG2P	cis	lung	GTEx
rs705866	PVRIG2P	cis	Thyroid	GTEx
rs705866	PILRB	cis	Muscle Skeletal	GTEx
rs705866	PILRB	cis	Adipose Subcutaneous	GTEx
rs705866	PILRB	cis	cerebellum	SCAN
rs705866	PVRIG2P	cis	Esophagus Muscularis	GTEx
rs705866	MEPCE	cis	lymphoblastoid	seeQTL
rs705866	PVRIG	cis	cerebellum	SCAN
rs705866	PILRA	cis	cerebellum	SCAN
rs705866	STAG3L5P	cis	Heart Left Ventricle	GTEx
rs705866	PVRIG2P	cis	Adipose Subcutaneous	GTEx
rs705866	PILRB	cis	multi-tissue	Pritchard
rs705866	PILRA	cis	Skin Sun Exposed Lower leg	GTEx
rs705866	PILRB	cis	Whole Blood	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99934000-99977600	Weak transcription	Fetal Brain Male	brain
2	chr7:99937600-99967800	Strong transcription	Fetal Stomach	stomach
3	chr7:99938600-99967400	Strong transcription	Fetal Brain Female	brain
4	chr7:99940800-100014600	Weak transcription	Right Atrium	heart
5	chr7:99942800-99966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:99942800-99966400	Strong transcription	A549	lung
7	chr7:99942800-99967000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr7:99942800-99967400	Strong transcription	Fetal Intestine Small	intestine
9	chr7:99943200-99965400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr7:99943400-99966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:99943400-99967200	Strong transcription	Fetal Intestine Large	intestine
12	chr7:99944000-99967000	Strong transcription	Brain Anterior Caudate	brain
13	chr7:99944200-99967400	Strong transcription	Brain Germinal Matrix	brain
14	chr7:99945400-99969400	Weak transcription	Fetal Heart	heart
15	chr7:99945600-99966000	Strong transcription	Fetal Muscle Leg	muscle
16	chr7:99946000-99966800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr7:99946400-99967400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr7:99957000-99966400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr7:99957200-99967000	Weak transcription	Stomach Mucosa	stomach
20	chr7:99957800-99965600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr7:99959600-99970200	Weak transcription	HSMM	muscle
22	chr7:99959800-99966800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr7:99960000-99967400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr7:99960200-99965400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:99960200-99966400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr7:99960200-99968400	Weak transcription	Gastric	stomach
27	chr7:99960200-99969000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr7:99960200-99975400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr7:99960400-99984800	Weak transcription	Pancreas	Pancrea
30	chr7:99960600-99967800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:99960600-99970000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr7:99960600-99975600	Weak transcription	Brain Angular Gyrus	brain
33	chr7:99960600-99977600	Weak transcription	Colon Smooth Muscle	Colon
34	chr7:99960600-99985200	Weak transcription	Aorta	Aorta
35	chr7:99960800-99971800	Weak transcription	HSMMtube	muscle
36	chr7:99960800-99976600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr7:99961200-99969600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr7:99961200-99969800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr7:99961200-99970000	Weak transcription	NHEK	skin
40	chr7:99961400-99967800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr7:99961400-99967800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:99961400-99969000	Weak transcription	Hela-S3	cervix
43	chr7:99961400-99969200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr7:99961400-99970000	Weak transcription	HUVEC	blood vessel
45	chr7:99961400-99977400	Weak transcription	Brain Substantia Nigra	brain
46	chr7:99961600-99970000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr7:99961600-99970400	Weak transcription	Fetal Lung	lung
48	chr7:99961600-99970600	Weak transcription	HepG2	liver
49	chr7:99962000-99967800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr7:99962000-99970200	Enhancers	Primary monocytes fromperipheralblood	blood

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