Variant report

Variant	rs1331634
Chromosome Location	chr6:146349405-146349406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10223507	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap]
rs1062067	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs1062068	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs10872582	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1133832	0.94[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap]
rs1832362	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2073287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[ASN][1000 genomes]
rs2144478	0.84[ASN][1000 genomes]
rs2224120	1.00[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap]
rs2224121	0.84[ASN][1000 genomes]
rs2243665	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2247317	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2247666	0.96[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs2249386	0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.80[TSI][hapmap]
rs2250387	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2253307	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs2253648	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2253654	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs2253764	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2253768	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2254283	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2254288	0.94[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap]
rs2256998	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs2265471	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2265472	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2265477	0.88[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap]
rs2265917	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2265919	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2328712	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2748483	0.86[ASN][1000 genomes]
rs2748484	0.86[ASN][1000 genomes]
rs2748486	0.82[ASN][1000 genomes]
rs2748502	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs2777477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2777484	0.86[ASN][1000 genomes]
rs2814863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap]
rs2814866	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2814874	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs2814875	1.00[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.98[TSI][hapmap]
rs2814877	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs2814880	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2892453	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3924499	0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs3924502	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs4075694	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs4075695	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs4243478	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4280983	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs4360151	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs6570723	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs6570736	0.81[ASN][1000 genomes]
rs6570738	0.81[ASN][1000 genomes]
rs6917135	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs6922507	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs6923545	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs6926076	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6930975	0.81[ASN][1000 genomes]
rs7739418	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7742333	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs7745696	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs7753092	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs7753696	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs7762562	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs854145	0.86[ASN][1000 genomes]
rs863820	1.00[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap]
rs9322046	0.81[ASN][1000 genomes]
rs9376970	0.96[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs9376971	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9386141	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs9390365	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs9403749	0.93[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap]
rs9403750	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs9403755	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs9403756	0.96[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs9403757	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9403765	0.84[ASN][1000 genomes]
rs9497424	0.94[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap]
rs9497425	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs9497427	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs9497431	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs9497434	0.92[CEU][hapmap];0.95[GIH][hapmap];0.85[TSI][hapmap]
rs9791313	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv604839	chr6:146305810-146828922	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1331634	SHPRH	cis	cerebellum	SCAN
rs1331634	SHPRH	cis	parietal	SCAN
rs1331634	ULBP3	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146348400-146351400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr6:146348600-146349600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:146348600-146349800	Active TSS	Brain Angular Gyrus	brain
4	chr6:146348600-146351200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
5	chr6:146348600-146351200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:146348600-146351400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:146348600-146351400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr6:146348600-146351600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr6:146348600-146351600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr6:146348800-146349600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:146348800-146349600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:146348800-146349600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:146348800-146349800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr6:146348800-146349800	Active TSS	Brain Anterior Caudate	brain
15	chr6:146348800-146349800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
16	chr6:146348800-146350000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:146348800-146350000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:146348800-146350000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:146348800-146350000	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr6:146348800-146350000	ZNF genes & repeats	Lung	lung
21	chr6:146348800-146350000	Enhancers	Pancreas	Pancrea
22	chr6:146348800-146350200	Active TSS	H9 Cell Line	embryonic stem cell
23	chr6:146348800-146350200	Bivalent/Poised TSS	Fetal Brain Female	brain
24	chr6:146348800-146350400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:146348800-146350800	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr6:146348800-146351200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
27	chr6:146348800-146351400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
28	chr6:146349000-146349600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
29	chr6:146349000-146349600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
30	chr6:146349000-146349600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr6:146349000-146350000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
32	chr6:146349000-146350400	Bivalent Enhancer	Fetal Muscle Leg	muscle
33	chr6:146349000-146351800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
34	chr6:146349200-146349600	Genic enhancers	Right Atrium	heart
35	chr6:146349200-146349600	Enhancers	Right Ventricle	heart
36	chr6:146349200-146349800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
37	chr6:146349200-146349800	Bivalent Enhancer	Fetal Heart	heart
38	chr6:146349200-146350000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:146349200-146350600	ZNF genes & repeats	Spleen	Spleen
40	chr6:146349400-146349600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:146349400-146349600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:146349400-146349600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:146349400-146349600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:146349400-146349600	Bivalent Enhancer	Brain Substantia Nigra	brain
45	chr6:146349400-146349600	Bivalent Enhancer	Left Ventricle	heart
46	chr6:146349400-146349600	Active TSS	NH-A	brain
47	chr6:146349400-146349800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:146349400-146349800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:146349400-146349800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:146349400-146349800	Bivalent/Poised TSS	Adipose Nuclei	Adipose

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