Variant report

Variant	rs35860312
Chromosome Location	chr3:52387078-52387079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52384981..52388271-chr3:52408939..52411277,3	K562	blood:
2	chr3:52310461..52311969-chr3:52386050..52388691,2	K562	blood:

Extended variants
information (count: 121 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap]
rs1011063	0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs1011064	1.00[JPT][hapmap]
rs1060330	0.80[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap]
rs1077142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][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]
rs10865972	1.00[JPT][hapmap]
rs11705963	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11706001	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11706108	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11707864	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs11707931	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11709658	0.86[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs11711934	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11714402	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716017	0.86[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs11716487	0.86[LWK][hapmap]
rs11717383	0.91[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap]
rs11718125	0.93[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721286	1.00[JPT][hapmap]
rs123598	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs123602	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs123603	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13059674	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13060192	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13071708	1.00[JPT][hapmap]
rs13075370	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs13076508	1.00[JPT][hapmap]
rs13076890	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089892	1.00[CHD][hapmap]
rs13091360	1.00[JPT][hapmap]
rs13091545	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1541495	1.00[JPT][hapmap]
rs164637	1.00[JPT][hapmap]
rs17052058	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17052061	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17052068	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2016575	0.93[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs2109558	1.00[JPT][hapmap]
rs2109559	1.00[JPT][hapmap]
rs2159607	0.93[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs2215466	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2276834	0.82[AFR][1000 genomes]
rs2335640	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28481563	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878549	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34238085	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34261027	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34355561	0.92[EUR][1000 genomes]
rs34523877	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34551211	1.00[JPT][hapmap]
rs34762015	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34908451	0.93[EUR][1000 genomes]
rs35133416	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs352142	1.00[JPT][hapmap]
rs352143	1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes]
rs352144	1.00[JPT][hapmap]
rs352173	1.00[JPT][hapmap]
rs353548	1.00[JPT][hapmap]
rs3752819	0.92[EUR][1000 genomes]
rs3755810	1.00[CHD][hapmap]
rs3774409	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3774410	1.00[JPT][hapmap]
rs3796343	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs390802	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs409803	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs419050	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs419604	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs419752	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4312651	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4687614	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4687617	1.00[JPT][hapmap]
rs4687618	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4687619	1.00[JPT][hapmap]
rs498778	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs498946	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55965068	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55997317	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56357549	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57441156	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59612757	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs610060	0.80[LWK][hapmap];0.87[MKK][hapmap]
rs61150019	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs613519	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs634382	0.81[ASW][hapmap];0.86[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6445358	0.93[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs6445386	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445486	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6445506	1.00[JPT][hapmap]
rs66462821	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67248391	0.93[EUR][1000 genomes]
rs676034	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6763882	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6771558	1.00[JPT][hapmap]
rs67834575	0.93[EUR][1000 genomes]
rs6784615	1.00[JPT][hapmap]
rs6794675	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6796333	0.93[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6800707	0.93[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6810027	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs728408	1.00[JPT][hapmap]
rs758803	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7614727	0.93[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap]
rs7620015	1.00[JPT][hapmap]
rs7622851	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs7629072	0.81[AFR][1000 genomes]
rs7643570	1.00[ASW][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs82825	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs887514	1.00[JPT][hapmap]
rs887515	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs929528	1.00[JPT][hapmap]
rs9311474	0.82[AFR][1000 genomes]
rs9844183	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9846089	1.00[JPT][hapmap]
rs9855470	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9861879	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9863753	1.00[JPT][hapmap]
rs9867823	1.00[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
2	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
4	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs35860312	ITIH3	cis	parietal	SCAN
rs35860312	DNAH1	cis	parietal	SCAN
rs35860312	SEMA3G	cis	cerebellum	SCAN
rs35860312	LOC286359	trans	parietal	SCAN
rs35860312	DNAH1	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52364800-52394400	Weak transcription	HSMMtube	muscle
2	chr3:52373800-52396000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:52374000-52399000	Weak transcription	Stomach Mucosa	stomach
4	chr3:52374000-52407000	Strong transcription	Fetal Intestine Small	intestine
5	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:52375400-52405600	Strong transcription	Lung	lung
7	chr3:52376400-52402000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:52377000-52406600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:52377000-52406600	Strong transcription	Liver	Liver
10	chr3:52377200-52390600	Strong transcription	Primary T cells from cord blood	blood
11	chr3:52377200-52405200	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:52377400-52397400	Strong transcription	Brain Inferior Temporal Lobe	brain
13	chr3:52377400-52404800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:52377400-52406600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:52377400-52406800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:52377600-52406200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr3:52377800-52406200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr3:52377800-52407200	Strong transcription	Fetal Intestine Large	intestine
19	chr3:52378200-52391600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr3:52378400-52400000	Strong transcription	Brain Anterior Caudate	brain
21	chr3:52378400-52401200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:52378400-52401200	Strong transcription	Gastric	stomach
23	chr3:52378400-52401800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:52378600-52389800	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:52378600-52390800	Strong transcription	Thymus	Thymus
26	chr3:52378600-52400000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:52378600-52400200	Strong transcription	Brain Cingulate Gyrus	brain
28	chr3:52378600-52400200	Strong transcription	Brain Hippocampus Middle	brain
29	chr3:52378600-52405000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr3:52378600-52406800	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:52379200-52389800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:52379200-52391000	Strong transcription	Primary B cells from cord blood	blood
33	chr3:52379400-52410600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:52380400-52401000	Strong transcription	Placenta	Placenta
35	chr3:52380800-52396400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:52381400-52401200	Strong transcription	Ovary	ovary
37	chr3:52381400-52402600	Strong transcription	Fetal Stomach	stomach
38	chr3:52381400-52404200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:52381400-52407400	Weak transcription	NHLF	lung
40	chr3:52381600-52392600	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:52381600-52396400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:52381600-52397600	Strong transcription	Stomach Smooth Muscle	stomach
43	chr3:52381600-52405400	Strong transcription	Adipose Nuclei	Adipose
44	chr3:52381600-52405800	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr3:52381800-52397000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:52382000-52389600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:52382000-52390000	Strong transcription	Right Ventricle	heart
48	chr3:52382200-52395800	Weak transcription	Psoas Muscle	Psoas
49	chr3:52382400-52396000	Strong transcription	Colonic Mucosa	Colon
50	chr3:52382600-52387600	Strong transcription	Primary hematopoietic stem cells	blood

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