Variant report

Variant	rs7311246
Chromosome Location	chr12:82870198-82870199
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 144 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs10506869	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506872	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10506873	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs10735453	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735454	0.83[YRI][hapmap]
rs10746242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746244	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778888	1.00[ASN][1000 genomes]
rs10778889	0.93[ASW][hapmap];1.00[CHB][hapmap];0.90[LWK][hapmap];0.85[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs10778895	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10778902	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778908	1.00[CHB][hapmap]
rs10862480	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10862482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11115240	1.00[ASN][1000 genomes]
rs11115241	1.00[ASN][1000 genomes]
rs11115242	1.00[ASN][1000 genomes]
rs11115308	1.00[ASN][1000 genomes]
rs11831879	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11832758	1.00[ASN][1000 genomes]
rs11835324	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11836773	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11837949	0.81[AFR][1000 genomes]
rs1494023	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1494024	1.00[CEU][hapmap];1.00[CHB][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]
rs1494027	1.00[CHB][hapmap]
rs17009629	0.81[AFR][1000 genomes]
rs17711838	1.00[ASN][1000 genomes]
rs17712868	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17712927	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17719063	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs17719970	1.00[ASN][1000 genomes]
rs17720305	1.00[ASN][1000 genomes]
rs17773938	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17774157	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs17774489	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17774872	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17775025	1.00[ASN][1000 genomes]
rs17775169	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs17776036	1.00[ASN][1000 genomes]
rs17776290	1.00[ASN][1000 genomes]
rs17776375	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17776885	1.00[ASN][1000 genomes]
rs2254688	0.84[YRI][hapmap]
rs2401034	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2401035	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642010	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642018	0.80[YRI][hapmap]
rs2642019	0.80[YRI][hapmap]
rs2717446	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731287	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731289	0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs2731290	0.80[YRI][hapmap]
rs2731291	0.80[YRI][hapmap]
rs2731294	0.85[AFR][1000 genomes]
rs2731295	0.81[LWK][hapmap]
rs2895914	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs2896434	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34638401	1.00[ASN][1000 genomes]
rs34775923	1.00[ASN][1000 genomes]
rs4143188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4319577	1.00[ASN][1000 genomes]
rs4411333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4491327	1.00[ASN][1000 genomes]
rs4495950	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.93[LWK][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882453	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882526	1.00[ASN][1000 genomes]
rs4882527	1.00[ASN][1000 genomes]
rs4882528	1.00[ASN][1000 genomes]
rs4882530	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57418508	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539659	1.00[ASN][1000 genomes]
rs6539662	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133956	0.93[AFR][1000 genomes]
rs7138488	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs7294780	1.00[ASN][1000 genomes]
rs7294918	1.00[ASN][1000 genomes]
rs7295042	1.00[ASN][1000 genomes]
rs7304084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306421	1.00[ASN][1000 genomes]
rs73149542	1.00[ASN][1000 genomes]
rs73149557	1.00[ASN][1000 genomes]
rs73149567	1.00[ASN][1000 genomes]
rs73149577	1.00[ASN][1000 genomes]
rs73149595	1.00[ASN][1000 genomes]
rs73149597	1.00[ASN][1000 genomes]
rs73151403	1.00[ASN][1000 genomes]
rs73151413	1.00[ASN][1000 genomes]
rs73151422	1.00[ASN][1000 genomes]
rs73151425	1.00[ASN][1000 genomes]
rs73151445	1.00[ASN][1000 genomes]
rs73151447	1.00[ASN][1000 genomes]
rs73151450	1.00[ASN][1000 genomes]
rs73151460	1.00[ASN][1000 genomes]
rs73151484	1.00[ASN][1000 genomes]
rs73151489	1.00[ASN][1000 genomes]
rs73151496	1.00[ASN][1000 genomes]
rs73153504	1.00[ASN][1000 genomes]
rs73153509	1.00[ASN][1000 genomes]
rs73153526	1.00[ASN][1000 genomes]
rs73153530	1.00[ASN][1000 genomes]
rs73153534	1.00[ASN][1000 genomes]
rs73153539	1.00[ASN][1000 genomes]
rs73153551	1.00[ASN][1000 genomes]
rs73153559	1.00[ASN][1000 genomes]
rs73153561	1.00[ASN][1000 genomes]
rs73153569	1.00[ASN][1000 genomes]
rs73153571	1.00[ASN][1000 genomes]
rs73153572	1.00[ASN][1000 genomes]
rs73153573	1.00[ASN][1000 genomes]
rs73153577	1.00[ASN][1000 genomes]
rs73153578	1.00[ASN][1000 genomes]
rs73153584	1.00[ASN][1000 genomes]
rs73153585	1.00[ASN][1000 genomes]
rs73153587	1.00[ASN][1000 genomes]
rs73153588	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73153590	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73153592	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73153599	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155404	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155406	1.00[ASN][1000 genomes]
rs73155441	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488252	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953161	0.83[AFR][1000 genomes]
rs7956163	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957993	1.00[ASN][1000 genomes]
rs7960966	1.00[ASN][1000 genomes]
rs7964174	1.00[ASN][1000 genomes]
rs7966041	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967097	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968024	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971746	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977442	1.00[ASW][hapmap];0.84[GIH][hapmap];0.86[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559539	chr12:82280797-82896218	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1041954	chr12:82314981-83008609	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv541550	chr12:82314981-83008609	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv559541	chr12:82715210-83108395	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv899348	chr12:82744187-83169297	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv1841396	chr12:82768717-82881082	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv519197	chr12:82831845-83056476	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7311246	RP11-263K4.3	cis	Thyroid	GTEx
rs7311246	C12orf26	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:82832400-82873400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:82834000-82874400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr12:82837800-82876400	Weak transcription	Psoas Muscle	Psoas
4	chr12:82862800-82873000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:82867200-82870600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:82867600-82870200	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:82867600-82873000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:82867800-82870400	Weak transcription	Left Ventricle	heart
9	chr12:82867800-82871000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr12:82867800-82872000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:82867800-82874400	Weak transcription	Primary B cells from cord blood	blood
12	chr12:82868000-82870400	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:82868000-82873000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:82868000-82874600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr12:82868200-82870800	Weak transcription	Fetal Lung	lung
16	chr12:82868200-82872000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr12:82868200-82872000	Weak transcription	GM12878-XiMat	blood
18	chr12:82868200-82873800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:82868400-82870200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr12:82868400-82870600	Weak transcription	Primary T cells from cord blood	blood
21	chr12:82868400-82870600	Weak transcription	Fetal Heart	heart
22	chr12:82868400-82871000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:82868400-82874000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:82868600-82873600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr12:82868800-82870600	Weak transcription	Fetal Intestine Large	intestine
26	chr12:82869000-82870400	Enhancers	HUVEC	blood vessel
27	chr12:82869000-82870600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:82869000-82872200	Weak transcription	Liver	Liver
29	chr12:82869000-82873000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:82869000-82876000	Weak transcription	Adipose Nuclei	Adipose
31	chr12:82869200-82873000	Weak transcription	NH-A	brain
32	chr12:82869200-82873200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:82869200-82873200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:82869200-82873200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:82869200-82873200	Weak transcription	NHEK	skin

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