Variant report

Variant	rs1982795
Chromosome Location	chr10:46041227-46041228
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10793618	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10793621	0.90[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1080264	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10900226	0.91[GIH][hapmap]
rs10900227	1.00[CEU][hapmap];0.97[GIH][hapmap]
rs11239558	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11239559	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11239564	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11239565	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11239567	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11239570	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239577	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11239585	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11239587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11528544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12217545	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12766066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1565096	0.88[EUR][1000 genomes]
rs1565097	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1982794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994426	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3740107	0.86[EUR][1000 genomes]
rs3824617	0.90[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4948673	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4949003	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4949006	0.82[GIH][hapmap]
rs7074524	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7095806	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73289207	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7896175	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs7900810	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7900977	0.91[EUR][1000 genomes]
rs7918454	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7920317	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430166	chr10:45668894-46148794	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv895108	chr10:45878908-46224333	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv895109	chr10:45882741-46210665	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv1043536	chr10:45915941-46076235	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv895111	chr10:45989745-46071900	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv895112	chr10:46012620-46202216	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv1041417	chr10:46021181-46088061	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv528750	chr10:46024620-46076235	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1052233	chr10:46024620-46088061	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1047117	chr10:46027942-46075946	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1982795	AGAP4	cis	Skin Sun Exposed Lower leg	GTEx
rs1982795	ZFAND4	cis	Nerve Tibial	GTEx
rs1982795	ANUBL1	cis	parietal	SCAN
rs1982795	AGAP4	cis	Whole Blood	GTEx
rs1982795	MARCH8	cis	cerebellum	SCAN
rs1982795	RBP3	cis	parietal	SCAN
rs1982795	AGAP4	cis	Artery Tibial	GTEx
rs1982795	ANUBL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46009400-46044400	Weak transcription	Thymus	Thymus
2	chr10:46010000-46056000	Weak transcription	Esophagus	oesophagus
3	chr10:46014400-46070000	Weak transcription	Psoas Muscle	Psoas
4	chr10:46015600-46043400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr10:46018000-46052800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr10:46022000-46043400	Weak transcription	Brain Angular Gyrus	brain
7	chr10:46022000-46046600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr10:46022200-46043600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr10:46024400-46052800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr10:46024600-46044600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr10:46026200-46057600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr10:46026400-46044400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr10:46027200-46043200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr10:46027200-46047000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr10:46028200-46042800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr10:46028200-46043200	Weak transcription	Brain Hippocampus Middle	brain
17	chr10:46028200-46044200	Weak transcription	Fetal Stomach	stomach
18	chr10:46028200-46044600	Weak transcription	Lung	lung
19	chr10:46028200-46053000	Weak transcription	Ovary	ovary
20	chr10:46028200-46055600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr10:46028400-46043600	Weak transcription	Brain Anterior Caudate	brain
22	chr10:46028400-46044600	Weak transcription	Adipose Nuclei	Adipose
23	chr10:46028400-46044600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr10:46028400-46044800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr10:46028400-46046600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr10:46028400-46052800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr10:46028800-46044600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr10:46028800-46044800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr10:46028800-46044800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr10:46028800-46052400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr10:46028800-46052600	Weak transcription	Left Ventricle	heart
32	chr10:46028800-46053000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr10:46028800-46069200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr10:46029200-46044800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr10:46030200-46044800	Weak transcription	Primary T cells from cord blood	blood
36	chr10:46030800-46043400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr10:46039200-46041400	Enhancers	Fetal Intestine Large	intestine
38	chr10:46039400-46041400	Enhancers	Fetal Intestine Small	intestine
39	chr10:46039600-46041400	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr10:46039600-46052600	Weak transcription	Spleen	Spleen
41	chr10:46040000-46054000	Weak transcription	Fetal Lung	lung
42	chr10:46040000-46056000	Weak transcription	Colonic Mucosa	Colon
43	chr10:46040200-46041400	Enhancers	Liver	Liver
44	chr10:46040200-46052400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr10:46040400-46041400	Enhancers	K562	blood
46	chr10:46040400-46056600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr10:46040600-46042000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr10:46040600-46042200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr10:46040800-46048600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr10:46040800-46050800	Weak transcription	Monocytes-CD14+_RO01746	blood

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