Variant report

Variant	rs6692233
Chromosome Location	chr1:84327214-84327215
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10127737	0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10465746	0.84[EUR][1000 genomes]
rs10493741	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs10493744	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs10874423	0.81[ASN][1000 genomes]
rs10874424	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs11163861	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11163862	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11163865	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11163866	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11163867	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs11163868	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs11163874	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11163875	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11163876	0.83[EUR][1000 genomes]
rs11163877	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs11163878	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11163879	0.83[EUR][1000 genomes]
rs11576870	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11580836	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11807807	0.83[EUR][1000 genomes]
rs12070578	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12118434	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12120160	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12121175	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12127266	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12133778	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12135028	1.00[JPT][hapmap]
rs12139191	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs12140068	0.84[EUR][1000 genomes]
rs12141272	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12145258	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs12146038	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12403631	1.00[JPT][hapmap]
rs12406984	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12407641	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12410617	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs12723239	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12730621	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12732697	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12748268	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12749350	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12757632	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs12758441	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12759527	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs1324484	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1324486	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs1359331	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1475263	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1536166	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1570690	0.81[EUR][1000 genomes]
rs1570691	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17099118	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs17475760	0.84[EUR][1000 genomes]
rs17534614	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1871924	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1871925	0.82[EUR][1000 genomes]
rs1925710	0.84[EUR][1000 genomes]
rs1952065	0.89[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs1952066	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs2024591	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2147950	0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs2224990	0.85[EUR][1000 genomes]
rs2389617	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2389647	0.85[EUR][1000 genomes]
rs2477201	0.85[JPT][hapmap]
rs28445286	0.84[EUR][1000 genomes]
rs28567085	0.85[EUR][1000 genomes]
rs28726372	0.87[ASN][1000 genomes]
rs35946036	0.84[EUR][1000 genomes]
rs35969331	0.84[EUR][1000 genomes]
rs4258241	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4907185	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4907186	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4907188	0.80[ASN][1000 genomes]
rs4907189	0.96[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4907191	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs5028806	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs558567	0.85[JPT][hapmap]
rs575633	0.85[JPT][hapmap]
rs598531	0.85[JPT][hapmap]
rs639666	0.85[JPT][hapmap]
rs6576956	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs663136	0.85[JPT][hapmap]
rs6658559	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6670658	0.83[EUR][1000 genomes]
rs6687372	0.84[EUR][1000 genomes]
rs6694752	0.82[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs6699501	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs670284	0.85[JPT][hapmap]
rs6703382	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6703493	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs685472	0.85[JPT][hapmap]
rs686839	0.85[JPT][hapmap]
rs7529293	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7531537	0.84[EUR][1000 genomes]
rs7550413	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs7551787	0.89[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs882897	0.89[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap]
rs942848	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs942849	0.85[EUR][1000 genomes]
rs9700285	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs980417	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs980418	0.83[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6692233	LPHN2	cis	parietal	SCAN
rs6692233	XM_089050	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84326800-84327400	Enhancers	Small Intestine	intestine
2	chr1:84326800-84327400	Enhancers	Stomach Mucosa	stomach
3	chr1:84326800-84330800	Weak transcription	HSMM	muscle
4	chr1:84326800-84348200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:84326800-84352600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:84327000-84327400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr1:84327000-84327400	Enhancers	Brain Angular Gyrus	brain
8	chr1:84327000-84327400	Enhancers	Brain Anterior Caudate	brain
9	chr1:84327000-84327400	Enhancers	Duodenum Mucosa	Duodenum
10	chr1:84327000-84327400	Enhancers	Fetal Heart	heart
11	chr1:84327000-84327400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:84327000-84327400	Enhancers	HMEC	breast
13	chr1:84327000-84327600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:84327000-84327600	Enhancers	Brain Substantia Nigra	brain
15	chr1:84327000-84327600	Enhancers	Osteobl	bone
16	chr1:84327000-84328800	Enhancers	Brain Hippocampus Middle	brain
17	chr1:84327000-84345000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:84327000-84348400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:84327000-84352400	Weak transcription	Aorta	Aorta
20	chr1:84327000-84361800	Weak transcription	Fetal Brain Female	brain
21	chr1:84327000-84375400	Weak transcription	Brain Germinal Matrix	brain
22	chr1:84327200-84327400	Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr1:84327200-84327400	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr1:84327200-84327400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
25	chr1:84327200-84327400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:84327200-84327400	Enhancers	NHEK	skin
27	chr1:84327200-84327600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:84327200-84327600	Enhancers	Liver	Liver
29	chr1:84327200-84327800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:84327200-84328600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:84327200-84348600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:84327200-84349600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:84327200-84351400	Weak transcription	Brain Inferior Temporal Lobe	brain

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