Variant report

Variant	rs2335640
Chromosome Location	chr3:52368387-52368388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 138 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap]
rs1011063	1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs1011064	1.00[JPT][hapmap]
rs10460962	0.83[ASW][hapmap];1.00[LWK][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes]
rs10461028	0.89[AFR][1000 genomes]
rs1077142	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]
rs10865972	1.00[JPT][hapmap]
rs11705963	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11706001	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706108	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11707864	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707931	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709658	0.93[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710014	0.91[LWK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs11711934	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11711974	0.86[LWK][hapmap]
rs11714402	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11716017	0.93[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718125	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11721286	1.00[JPT][hapmap]
rs123598	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs123602	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs123603	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13059674	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13060192	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13071708	1.00[JPT][hapmap]
rs13075370	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076508	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13076890	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13089892	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs13091360	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13091545	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13096571	1.00[ASN][1000 genomes]
rs1541495	1.00[JPT][hapmap]
rs164637	1.00[JPT][hapmap]
rs17052053	0.83[ASW][hapmap];0.97[LWK][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes]
rs17052054	0.83[ASW][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs17052058	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17052061	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17052068	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016575	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2109557	1.00[ASN][1000 genomes]
rs2109558	1.00[JPT][hapmap]
rs2109559	1.00[JPT][hapmap]
rs2159607	0.87[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs2215466	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs28481563	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2878549	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34181173	1.00[ASN][1000 genomes]
rs34238085	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34261027	0.81[EUR][1000 genomes]
rs34332947	1.00[ASN][1000 genomes]
rs34355561	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34523877	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34551211	1.00[JPT][hapmap]
rs34628357	1.00[ASN][1000 genomes]
rs34762015	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34827613	1.00[ASN][1000 genomes]
rs34908451	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35133416	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352142	1.00[JPT][hapmap]
rs352143	1.00[JPT][hapmap]
rs352144	1.00[JPT][hapmap]
rs352173	1.00[JPT][hapmap]
rs353548	1.00[JPT][hapmap]
rs35860312	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]
rs35982798	1.00[ASN][1000 genomes]
rs3733063	0.82[LWK][hapmap];0.82[YRI][hapmap]
rs3752819	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755810	1.00[CHD][hapmap]
rs3774409	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3774410	1.00[JPT][hapmap]
rs3796343	0.86[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs390802	0.93[CEU][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs4082828	0.83[LWK][hapmap]
rs409803	1.00[JPT][hapmap]
rs419050	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs419604	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs419752	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
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];1.00[ASN][1000 genomes]
rs498946	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55965068	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55997317	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56352611	0.93[AFR][1000 genomes]
rs56357549	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57441156	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs575476	1.00[ASN][1000 genomes]
rs59612757	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61150019	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613519	1.00[JPT][hapmap]
rs61734640	1.00[ASN][1000 genomes]
rs634382	1.00[JPT][hapmap];0.84[TSI][hapmap]
rs6445385	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs6445386	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6445486	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6445506	1.00[JPT][hapmap]
rs66462821	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67248391	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676034	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6763882	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6771558	1.00[JPT][hapmap]
rs67834575	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784615	1.00[JPT][hapmap]
rs6793317	0.80[LWK][hapmap]
rs6794675	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795333	1.00[ASN][1000 genomes]
rs6796333	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6800707	0.87[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6810027	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs71297391	1.00[ASN][1000 genomes]
rs71297394	1.00[ASN][1000 genomes]
rs71297395	1.00[ASN][1000 genomes]
rs71297396	1.00[ASN][1000 genomes]
rs728408	1.00[JPT][hapmap]
rs73088800	0.93[AFR][1000 genomes]
rs758803	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7615405	0.86[AFR][1000 genomes]
rs7620015	1.00[JPT][hapmap]
rs7643570	0.81[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs82825	0.92[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs887514	1.00[JPT][hapmap]
rs887515	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs929528	1.00[JPT][hapmap]
rs9844183	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9846089	1.00[JPT][hapmap]
rs9855470	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9861879	0.82[AMR][1000 genomes];0.93[EUR][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
rs2335640	SEMA3G	cis	cerebellum	SCAN
rs2335640	DNAH1	cis	cerebellum	SCAN
rs2335640	DNAH1	cis	parietal	SCAN
rs2335640	PPM1M	cis	parietal	SCAN
rs2335640	ITIH3	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:52344600-52378600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:52352000-52379800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:52352200-52370800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:52352200-52379000	Weak transcription	Colonic Mucosa	Colon
6	chr3:52352200-52382000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:52352200-52384600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:52352600-52373400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:52352600-52379400	Weak transcription	Pancreas	Pancrea
10	chr3:52353400-52377400	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:52354400-52379800	Weak transcription	Esophagus	oesophagus
12	chr3:52354800-52384000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:52358200-52372000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:52358400-52370200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:52358400-52380400	Weak transcription	Ovary	ovary
16	chr3:52360400-52376200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:52361800-52368400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr3:52362200-52375000	Weak transcription	Fetal Thymus	thymus
19	chr3:52362400-52378200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:52362800-52378600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:52364200-52368600	Strong transcription	Primary T cells from cord blood	blood
22	chr3:52364200-52375800	Weak transcription	GM12878-XiMat	blood
23	chr3:52364200-52383000	Weak transcription	Fetal Lung	lung
24	chr3:52364400-52379400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:52364600-52368800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:52364800-52368400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:52364800-52368600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:52364800-52373400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:52364800-52373400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:52364800-52394400	Weak transcription	HSMMtube	muscle
31	chr3:52365000-52368800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:52365000-52368800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:52365000-52372200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:52365200-52368600	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr3:52365200-52368800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr3:52365200-52368800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr3:52365200-52368800	Strong transcription	Liver	Liver
38	chr3:52365200-52368800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr3:52365200-52368800	Strong transcription	Placenta	Placenta
40	chr3:52365400-52368800	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr3:52365800-52368400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr3:52365800-52368800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:52366000-52368400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:52366000-52368400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr3:52366000-52368800	Strong transcription	Adipose Nuclei	Adipose
46	chr3:52366200-52368800	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:52366400-52373800	Weak transcription	Fetal Brain Male	brain
48	chr3:52366400-52378400	Weak transcription	Brain Anterior Caudate	brain
49	chr3:52366400-52383000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:52366600-52370200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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