Variant report

Variant	rs10877324
Chromosome Location	chr12:60041477-60041478
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1027477	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10506397	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs10877321	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877323	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][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];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173101	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11173108	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17122696	1.00[CHB][hapmap]
rs17122765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17122775	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs4304824	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7965740	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs982322	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv899131	chr12:59942122-60124089	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1048949	chr12:59974039-60041477	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10877324	STAT6	cis	cerebellum	SCAN
rs10877324	ARHGEF25	cis	parietal	SCAN
rs10877324	RDH5	cis	parietal	SCAN
rs10877324	COPZ1	cis	parietal	SCAN
rs10877324	CTDSP2	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60013600-60055400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr12:60018800-60044400	Weak transcription	Pancreas	Pancrea
3	chr12:60020800-60044800	Weak transcription	NHDF-Ad	bronchial
4	chr12:60022400-60044800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:60026600-60089200	Weak transcription	Gastric	stomach
6	chr12:60028200-60051400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:60028400-60042800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr12:60029600-60063200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:60031000-60044200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:60031800-60044400	Weak transcription	Left Ventricle	heart
11	chr12:60031800-60050600	Weak transcription	Spleen	Spleen
12	chr12:60032000-60044200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:60032200-60043200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:60034000-60061600	Weak transcription	Aorta	Aorta
15	chr12:60035000-60044800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:60036400-60045000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:60037400-60042200	Strong transcription	Primary T cells from cord blood	blood
18	chr12:60037400-60045200	Weak transcription	Hela-S3	cervix
19	chr12:60037600-60044600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:60038000-60044200	Weak transcription	Fetal Heart	heart
21	chr12:60038000-60044400	Weak transcription	Esophagus	oesophagus
22	chr12:60038200-60042000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:60038200-60045400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:60039000-60042400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr12:60039000-60044400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:60039200-60043000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:60040200-60044400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr12:60040200-60048800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr12:60040200-60049000	Weak transcription	Dnd41	blood
30	chr12:60040200-60049800	Weak transcription	Primary B cells from cord blood	blood
31	chr12:60040400-60044200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr12:60040400-60050000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr12:60040400-60050000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr12:60040600-60041800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:60040600-60041800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:60040600-60044400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:60040600-60045200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:60040600-60048600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:60040600-60050400	Weak transcription	Right Ventricle	heart
40	chr12:60040600-60052400	Weak transcription	Lung	lung
41	chr12:60040600-60054000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:60040800-60045200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:60040800-60050000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:60040800-60054000	Weak transcription	Fetal Thymus	thymus
45	chr12:60041000-60044400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:60041200-60042600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr12:60041200-60044800	Weak transcription	HUVEC	blood vessel
48	chr12:60041200-60051400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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