Variant report

Variant	rs11050203
Chromosome Location	chr12:29491131-29491132
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10082956	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10128781	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs1035606	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1035607	0.87[EUR][1000 genomes]
rs10743657	0.83[AFR][1000 genomes]
rs10743658	0.83[AFR][1000 genomes]
rs10843390	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10843391	0.86[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10843397	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843398	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs10843403	0.82[AFR][1000 genomes]
rs11050175	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11050209	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1156242	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12320212	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12831751	0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2278093	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2278094	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs3782513	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3815843	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931178	0.83[AFR][1000 genomes]
rs6487815	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7136223	0.83[AMR][1000 genomes]
rs7297435	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7311742	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7315504	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9651802	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs966540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs966541	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs996498	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9989017	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11050203	RP11-996F15.2	cis	Artery Tibial	GTEx
rs11050203	RP11-996F15.2	cis	Thyroid	GTEx
rs11050203	ERGIC2	cis	multi-tissue	Pritchard
rs11050203	RP11-996F15.2	cis	Muscle Skeletal	GTEx
rs11050203	RP11-996F15.2	cis	Whole Blood	GTEx
rs11050203	RP11-996F15.2	cis	Esophagus Muscularis	GTEx
rs11050203	RP11-996F15.2	cis	Stomach	GTEx
rs11050203	RP11-996F15.2	cis	lung	GTEx
rs11050203	RP11-996F15.2	cis	Artery Aorta	GTEx
rs11050203	MLSTD1	cis	normal skin	skin_eQTL
rs11050203	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11050203	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs11050203	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs11050203	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
2	chr12:29452800-29494200	Weak transcription	Lung	lung
3	chr12:29459400-29493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
5	chr12:29465000-29494200	Weak transcription	Colonic Mucosa	Colon
6	chr12:29470000-29495600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:29470000-29500000	Weak transcription	K562	blood
8	chr12:29470800-29492800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr12:29470800-29492800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:29470800-29493400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:29470800-29493800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr12:29470800-29496000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:29470800-29508400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:29470800-29532800	Weak transcription	Right Ventricle	heart
15	chr12:29471200-29491400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr12:29471200-29493000	Weak transcription	Brain Substantia Nigra	brain
17	chr12:29471200-29494400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr12:29471400-29495800	Weak transcription	Brain Anterior Caudate	brain
19	chr12:29471600-29492600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:29472200-29493800	Weak transcription	Left Ventricle	heart
21	chr12:29473800-29493000	Weak transcription	HMEC	breast
22	chr12:29473800-29522600	Weak transcription	NHEK	skin
23	chr12:29474000-29493400	Weak transcription	HUVEC	blood vessel
24	chr12:29474200-29493000	Weak transcription	Osteobl	bone
25	chr12:29474200-29494200	Weak transcription	NHDF-Ad	bronchial
26	chr12:29474800-29493800	Weak transcription	Fetal Intestine Large	intestine
27	chr12:29475800-29491200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr12:29475800-29493200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr12:29475800-29493400	Weak transcription	Colon Smooth Muscle	Colon
30	chr12:29476000-29492200	Weak transcription	Placenta	Placenta
31	chr12:29476000-29496000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr12:29476000-29502600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:29476200-29493800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr12:29476200-29509400	Weak transcription	Spleen	Spleen
35	chr12:29476200-29512800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:29476200-29533400	Weak transcription	Pancreas	Pancrea
37	chr12:29476400-29491200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:29476400-29491200	Weak transcription	Fetal Thymus	thymus
39	chr12:29476400-29493000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:29476400-29493600	Weak transcription	Primary T cells from cord blood	blood
41	chr12:29476400-29494200	Weak transcription	Fetal Stomach	stomach
42	chr12:29476400-29498600	Weak transcription	Ovary	ovary
43	chr12:29476400-29509600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr12:29476400-29532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:29476400-29533200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:29476600-29492800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:29476600-29494200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:29476600-29499200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr12:29477000-29492400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:29477000-29493800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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