Variant report

Variant	rs807931
Chromosome Location	chr3:47389317-47389318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47374984..47378257-chr3:47387445..47390944,5	K562	blood:
2	chr3:47374984..47381273-chr3:47386586..47390760,8	K562	blood:
3	chr3:47388953..47390656-chr3:47391325..47392901,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL18-2	chr3:47388823-47390563	NONHSAT089495

Extended variants
information (count: 92 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1038394	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1076394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs10865946	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130123	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs11130124	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.98[TSI][hapmap]
rs11130126	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs11130127	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130128	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs11130129	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs11130137	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap]
rs11705957	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs11710013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs11710121	0.85[CEU][hapmap]
rs11710322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs11711265	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap]
rs11711824	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11712445	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11716763	0.96[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs11719877	0.96[CEU][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11915074	0.92[CEU][hapmap]
rs11920853	0.92[CEU][hapmap]
rs11925823	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11927371	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12486969	0.86[EUR][1000 genomes]
rs12487736	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12495169	0.85[JPT][hapmap]
rs12497225	0.87[EUR][1000 genomes]
rs12632132	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12636851	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs13059519	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs13064843	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13075233	0.96[CEU][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13079098	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13094438	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs1531875	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1638676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs17080872	0.81[JPT][hapmap]
rs17410853	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs17411375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17784882	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs1872164	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs2062278	0.87[EUR][1000 genomes]
rs2101247	0.92[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs2132173	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs2159400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276853	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap]
rs2276854	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs2291298	0.96[CEU][hapmap]
rs295428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs295442	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs295449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3736177	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs3816779	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap]
rs4241548	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4683326	1.00[CEU][hapmap]
rs4858805	0.86[EUR][1000 genomes]
rs4858811	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs4858824	0.96[CEU][hapmap]
rs4858848	0.85[EUR][1000 genomes]
rs4858868	0.96[CEU][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4858888	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858890	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858893	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs4858894	0.87[CEU][hapmap];0.88[JPT][hapmap]
rs553989	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56032309	0.87[EUR][1000 genomes]
rs56351005	0.86[EUR][1000 genomes]
rs57346147	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60369822	0.81[EUR][1000 genomes]
rs62246474	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6768221	0.92[CEU][hapmap]
rs6772670	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs6780013	0.89[CEU][hapmap];0.86[TSI][hapmap]
rs6787422	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6791842	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap]
rs6792461	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs6800271	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7613282	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641010	0.83[EUR][1000 genomes]
rs7651762	0.96[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs807810	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs807932	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs807936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs811115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs8180040	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs878659	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs922957	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs9683033	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs807931	AMIGO3	cis	cerebellum	SCAN
rs807931	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs807931	CCDC12	cis	cerebellum	SCAN
rs807931	HYAL2	cis	cerebellum	SCAN
rs807931	CCHCR1	trans	lymphoblastoid	seeQTL
rs807931	RTP3	cis	lesional skin	skin_eQTL
rs807931	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs807931	PRKAR2A	cis	cerebellum	SCAN
rs807931	C3orf75	cis	cerebellum	SCAN
rs807931	SCAP	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47361400-47389800	Weak transcription	Right Atrium	heart
2	chr3:47376600-47389400	Weak transcription	Fetal Lung	lung
3	chr3:47381800-47389600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:47386200-47395600	Weak transcription	Ovary	ovary
5	chr3:47386400-47389600	Enhancers	Primary hematopoietic stem cells	blood
6	chr3:47386800-47390400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:47386800-47400800	Weak transcription	Pancreas	Pancrea
8	chr3:47387000-47389400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:47387000-47389400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:47387000-47390200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr3:47387000-47390400	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:47387000-47390400	Weak transcription	Gastric	stomach
13	chr3:47387000-47390600	Weak transcription	Thymus	Thymus
14	chr3:47387200-47389400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:47387400-47389600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr3:47387400-47389600	Weak transcription	Liver	Liver
17	chr3:47387600-47390400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:47387600-47397200	Weak transcription	Lung	lung
19	chr3:47387800-47389400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:47387800-47389400	Weak transcription	Dnd41	blood
21	chr3:47387800-47389400	Enhancers	NHDF-Ad	bronchial
22	chr3:47387800-47389600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:47387800-47389600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:47387800-47389600	Enhancers	HSMMtube	muscle
25	chr3:47388000-47389400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:47388000-47389400	Enhancers	HSMM	muscle
27	chr3:47388000-47389600	Weak transcription	Brain Angular Gyrus	brain
28	chr3:47388000-47389600	Enhancers	NHLF	lung
29	chr3:47388000-47389800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:47388000-47389800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:47388000-47389800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:47388000-47389800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:47388000-47389800	Enhancers	Primary B cells from peripheral blood	blood
34	chr3:47388000-47390200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:47388000-47390600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:47388000-47391000	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:47388000-47394800	Weak transcription	Left Ventricle	heart
38	chr3:47388000-47397200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:47388000-47400600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:47388200-47389400	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr3:47388200-47389400	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr3:47388200-47389400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:47388200-47389800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:47388200-47389800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:47388200-47389800	Weak transcription	Brain Anterior Caudate	brain
46	chr3:47388200-47390000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr3:47388200-47390400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:47388200-47390400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:47388200-47390400	Weak transcription	Fetal Intestine Large	intestine
50	chr3:47388200-47391000	Weak transcription	Fetal Intestine Small	intestine

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