Variant report

Variant	rs7610636
Chromosome Location	chr3:47064436-47064437
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10433549	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs10461018	0.92[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs1079276	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1108301	0.92[EUR][1000 genomes]
rs11130110	0.92[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130111	0.92[CEU][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130112	0.92[CEU][hapmap];0.98[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs11130114	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130115	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs11707736	0.84[EUR][1000 genomes]
rs11708451	0.81[EUR][1000 genomes]
rs11709660	0.86[EUR][1000 genomes]
rs11712716	0.81[EUR][1000 genomes]
rs11715121	0.86[EUR][1000 genomes]
rs11716539	0.81[EUR][1000 genomes]
rs11716553	0.86[EUR][1000 genomes]
rs11719795	0.81[JPT][hapmap]
rs11720139	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs11917361	0.87[EUR][1000 genomes]
rs11917474	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12152493	0.90[EUR][1000 genomes]
rs12491473	0.88[EUR][1000 genomes]
rs12629262	0.81[EUR][1000 genomes]
rs12630534	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12715421	0.86[EUR][1000 genomes]
rs13061071	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13062022	0.80[EUR][1000 genomes]
rs13062681	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13066214	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13077398	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13084117	0.81[EUR][1000 genomes]
rs13087426	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13091054	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13094672	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13098228	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1463393	0.88[EUR][1000 genomes]
rs1466741	0.84[CEU][hapmap]
rs17784127	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs1869869	0.92[EUR][1000 genomes]
rs1869871	0.83[EUR][1000 genomes]
rs2061197	0.92[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2132173	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs2278963	0.89[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs2290546	0.81[JPT][hapmap]
rs2305634	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305635	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs2305638	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385867	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34103310	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34344887	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4078466	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4082155	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4234465	0.92[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs4587	0.81[JPT][hapmap]
rs4682831	0.92[EUR][1000 genomes]
rs4682837	0.92[CEU][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4682844	0.92[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs4682852	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs4683297	0.81[JPT][hapmap]
rs4683298	0.81[JPT][hapmap]
rs4683320	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683322	0.89[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs55724164	0.90[EUR][1000 genomes]
rs55843455	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55927279	0.86[EUR][1000 genomes]
rs56217494	0.85[EUR][1000 genomes]
rs56249396	0.88[EUR][1000 genomes]
rs61729713	0.92[EUR][1000 genomes]
rs62246375	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62246398	0.89[EUR][1000 genomes]
rs62248439	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6414435	0.84[EUR][1000 genomes]
rs6442040	0.81[JPT][hapmap]
rs6442055	0.85[EUR][1000 genomes]
rs66539935	0.92[EUR][1000 genomes]
rs66564457	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6763236	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6767218	0.89[EUR][1000 genomes]
rs6767907	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs6768722	0.86[EUR][1000 genomes]
rs6772670	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs6774733	0.89[EUR][1000 genomes]
rs6777145	0.85[EUR][1000 genomes]
rs6785790	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6794193	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6808742	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7433300	0.85[CEU][hapmap]
rs749511	0.89[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs749512	0.82[CEU][hapmap]
rs7610620	0.83[EUR][1000 genomes]
rs7617689	0.88[EUR][1000 genomes]
rs7621911	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7625067	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7625070	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7628747	0.92[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs7633435	0.81[EUR][1000 genomes]
rs7633698	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7636252	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7637302	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7640397	0.89[EUR][1000 genomes]
rs7645278	0.81[JPT][hapmap]
rs9311403	0.92[CEU][hapmap]
rs9837343	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs9844122	0.85[EUR][1000 genomes]
rs9845728	0.85[EUR][1000 genomes]
rs9852082	0.81[JPT][hapmap]
rs9854790	0.85[EUR][1000 genomes]
rs9855938	0.81[JPT][hapmap]
rs9858443	0.86[EUR][1000 genomes]
rs9875235	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	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
5	nsv997261	chr3:47054766-47133680	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7610636	HYAL2	cis	cerebellum	SCAN
rs7610636	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs7610636	RTP3	cis	lesional skin	skin_eQTL
rs7610636	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs7610636	SCAP	cis	parietal	SCAN
rs7610636	PRKAR2A	cis	cerebellum	SCAN
rs7610636	CCDC12	cis	cerebellum	SCAN
rs7610636	C3orf75	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47057200-47066600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:47058800-47069800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:47059400-47066400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:47059400-47066400	Strong transcription	Primary T cells from cord blood	blood
5	chr3:47059800-47067200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr3:47059800-47073000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:47060000-47064800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:47060000-47066400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr3:47060400-47066600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:47060600-47073800	Weak transcription	Lung	lung
11	chr3:47061000-47076200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:47061000-47079000	Weak transcription	Fetal Brain Male	brain
13	chr3:47061200-47069600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:47061200-47069800	Weak transcription	Spleen	Spleen
15	chr3:47061200-47072400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr3:47061200-47076000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:47061200-47083000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:47061400-47065800	Strong transcription	Fetal Thymus	thymus
19	chr3:47061400-47066400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:47061400-47069600	Weak transcription	HMEC	breast
21	chr3:47061400-47073600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:47061400-47074600	Weak transcription	Hela-S3	cervix
23	chr3:47061400-47076000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:47061400-47076200	Weak transcription	HSMMtube	muscle
25	chr3:47061600-47066200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:47061600-47066400	Weak transcription	NH-A	brain
27	chr3:47061800-47066200	Weak transcription	Brain Angular Gyrus	brain
28	chr3:47061800-47066400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:47061800-47066600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:47061800-47069800	Weak transcription	Placenta	Placenta
31	chr3:47061800-47074200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr3:47061800-47074600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr3:47062000-47064600	Enhancers	Stomach Smooth Muscle	stomach
34	chr3:47062000-47066400	Weak transcription	Brain Anterior Caudate	brain
35	chr3:47062000-47066600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:47062000-47069600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr3:47062000-47069600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:47062000-47069600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr3:47062000-47070200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:47062000-47071800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:47062000-47075400	Weak transcription	A549	lung
42	chr3:47062200-47066000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:47062200-47066400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:47062200-47066400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:47062200-47069600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:47062200-47069600	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:47062200-47070200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:47062200-47073400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:47062200-47073400	Weak transcription	GM12878-XiMat	blood
50	chr3:47062200-47075000	Weak transcription	Brain Germinal Matrix	brain

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