Variant report

Variant	rs12294037
Chromosome Location	chr11:72807631-72807632
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11235620	0.83[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs11822039	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs12419915	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1612659	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1783575	0.91[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2187494	0.82[GIH][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2366256	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3862796	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4394861	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4400839	0.83[CEU][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs4944823	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs593753	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6592500	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6592505	0.91[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs6592509	0.91[CEU][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6592510	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7102253	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7108955	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7124723	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422418	chr11:72646518-72807865	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12294037	FGF4	cis	cerebellum	SCAN
rs12294037	ATG16L2	cis	parietal	SCAN
rs12294037	STARD10	cis	multi-tissue	Pritchard
rs12294037	KCNE3	cis	cerebellum	SCAN
rs12294037	STARD10	cis	Whole Blood	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72746600-72824600	Weak transcription	Thymus	Thymus
2	chr11:72764200-72824600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr11:72773000-72810800	Weak transcription	Fetal Stomach	stomach
4	chr11:72773400-72810400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:72782600-72825200	Weak transcription	Lung	lung
6	chr11:72784600-72810800	Weak transcription	Aorta	Aorta
7	chr11:72784600-72812000	Weak transcription	NHEK	skin
8	chr11:72785000-72811000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:72785200-72810600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:72786200-72823600	Weak transcription	Placenta	Placenta
11	chr11:72788200-72825400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:72789200-72825000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr11:72789200-72825200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:72789400-72817600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr11:72789400-72825200	Weak transcription	HSMM	muscle
16	chr11:72789400-72825800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr11:72789600-72813400	Weak transcription	Fetal Intestine Large	intestine
18	chr11:72793200-72810600	Weak transcription	Fetal Intestine Small	intestine
19	chr11:72793200-72824800	Weak transcription	Dnd41	blood
20	chr11:72793600-72850600	Weak transcription	NH-A	brain
21	chr11:72795000-72824800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:72795600-72813600	Weak transcription	Primary T cells from cord blood	blood
23	chr11:72795600-72836000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr11:72795800-72812000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:72798200-72809800	Weak transcription	Liver	Liver
26	chr11:72798200-72824600	Weak transcription	HepG2	liver
27	chr11:72799200-72810000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr11:72799200-72810000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr11:72799200-72810000	Weak transcription	Spleen	Spleen
30	chr11:72799200-72810600	Weak transcription	Right Ventricle	heart
31	chr11:72799200-72825400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:72799400-72829400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr11:72799600-72814200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:72804400-72810000	Weak transcription	Fetal Muscle Leg	muscle
35	chr11:72804400-72820800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:72804600-72825200	Weak transcription	HSMMtube	muscle
37	chr11:72804800-72810000	Weak transcription	Fetal Thymus	thymus
38	chr11:72805400-72810200	Weak transcription	HUVEC	blood vessel
39	chr11:72806200-72807800	Enhancers	Brain Cingulate Gyrus	brain
40	chr11:72806400-72807800	Enhancers	Colon Smooth Muscle	Colon
41	chr11:72806400-72807800	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr11:72806600-72807800	Genic enhancers	Primary B cells from peripheral blood	blood
43	chr11:72806600-72807800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:72806600-72807800	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr11:72806600-72808000	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr11:72806600-72808400	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr11:72806600-72808400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr11:72806600-72826000	Weak transcription	Fetal Brain Male	brain
49	chr11:72806800-72807800	Enhancers	Primary hematopoietic stem cells	blood
50	chr11:72806800-72810000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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