Variant report

Variant	rs11050084
Chromosome Location	chr12:29310302-29310303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10743645	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10743647	0.83[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10743648	0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10743649	0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10771486	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10771489	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10771492	0.91[CEU][hapmap];0.82[CHB][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10771494	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10843343	0.86[EUR][1000 genomes]
rs11050098	0.91[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11050099	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11050104	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050108	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050110	0.91[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050112	0.91[CEU][hapmap];0.82[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11050114	0.83[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12310732	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12319200	0.91[CEU][hapmap]
rs12366549	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1496218	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1561131	1.00[JPT][hapmap]
rs1561132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1826800	0.83[CEU][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1845819	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1908690	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1908691	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2349971	1.00[JPT][hapmap]
rs2349974	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4105125	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4105126	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4105127	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4105128	0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4141943	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4141945	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4323913	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4536271	0.86[ASN][1000 genomes]
rs4930856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930857	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4930858	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4930859	0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4931158	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4931162	0.83[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4931163	0.83[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4931165	0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60287933	0.86[ASN][1000 genomes]
rs6487778	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6487783	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71453727	0.88[ASN][1000 genomes]
rs7294355	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7296268	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7297542	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7309041	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs7309881	0.90[CEU][hapmap];0.82[CHB][hapmap]
rs73265795	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7968949	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7974769	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7975191	0.89[EUR][1000 genomes]
rs7980923	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs924105	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs924107	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs924109	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs958478	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[EUR][1000 genomes];0.84[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11050084	ERGIC2	cis	parietal	SCAN
rs11050084	IFLTD1	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29303400-29311400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:29303400-29312200	Weak transcription	Spleen	Spleen
3	chr12:29303400-29316600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:29303400-29317000	Weak transcription	Colonic Mucosa	Colon
5	chr12:29303400-29317800	Weak transcription	Fetal Kidney	kidney
6	chr12:29303600-29313400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:29304000-29312600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:29306000-29312400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:29306400-29310400	Weak transcription	Right Atrium	heart
10	chr12:29306400-29313000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr12:29306400-29313200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:29306600-29310400	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr12:29306600-29310600	Weak transcription	Adipose Nuclei	Adipose
14	chr12:29306600-29312600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:29306600-29312600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:29306600-29313000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:29306600-29324600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:29306800-29310400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:29306800-29313200	Weak transcription	Fetal Thymus	thymus
20	chr12:29306800-29324400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:29308400-29312600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:29308400-29312600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:29308400-29312600	Weak transcription	K562	blood
24	chr12:29308400-29313200	Weak transcription	Brain Anterior Caudate	brain
25	chr12:29308400-29317000	Weak transcription	Fetal Intestine Small	intestine
26	chr12:29308400-29324000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:29308400-29324400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:29308600-29310400	Weak transcription	Placenta	Placenta
29	chr12:29308600-29311200	Weak transcription	GM12878-XiMat	blood
30	chr12:29308600-29312600	Weak transcription	Small Intestine	intestine
31	chr12:29308800-29317200	Weak transcription	Dnd41	blood
32	chr12:29309000-29310400	Enhancers	Primary hematopoietic stem cells	blood
33	chr12:29309200-29312600	Enhancers	HUVEC	blood vessel
34	chr12:29309400-29311400	Active TSS	Brain Hippocampus Middle	brain
35	chr12:29309400-29314400	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr12:29309600-29311600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr12:29309800-29311000	Enhancers	Primary B cells from cord blood	blood
38	chr12:29309800-29311400	Enhancers	NHDF-Ad	bronchial
39	chr12:29309800-29312000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:29310200-29310400	Active TSS	Brain Substantia Nigra	brain
41	chr12:29310200-29310400	Flanking Active TSS	NH-A	brain
42	chr12:29310200-29310800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:29310200-29310800	Enhancers	NHEK	skin
44	chr12:29310200-29311000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr12:29310200-29311000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:29310200-29311000	Enhancers	HMEC	breast
47	chr12:29310200-29311400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:29310200-29311600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:29310200-29311600	Enhancers	Osteobl	bone
50	chr12:29310200-29313400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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