Variant report

Variant	rs11050175
Chromosome Location	chr12:29455496-29455497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1035607	0.86[EUR][1000 genomes]
rs10843390	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs10843397	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11050203	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	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12320212	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278093	0.83[CEU][hapmap]
rs3782513	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3815843	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7297435	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7311742	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7953619	0.83[CEU][hapmap]
rs966540	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs966541	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs996498	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9989017	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11050175	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs11050175	RP11-996F15.2	cis	Muscle Skeletal	GTEx
rs11050175	RP11-996F15.2	cis	Thyroid	GTEx
rs11050175	RP11-996F15.2	cis	Esophagus Muscularis	GTEx
rs11050175	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11050175	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs11050175	MLSTD1	cis	normal skin	skin_eQTL
rs11050175	RP11-996F15.2	cis	lung	GTEx
rs11050175	RP11-996F15.2	cis	Artery Tibial	GTEx
rs11050175	RP11-996F15.2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29417200-29465400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:29422000-29455600	Weak transcription	Left Ventricle	heart
3	chr12:29422000-29465000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:29426800-29472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
6	chr12:29429000-29460200	Weak transcription	Primary T cells from cord blood	blood
7	chr12:29429200-29463600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:29429400-29460400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:29435400-29467200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:29439600-29464000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:29439600-29469400	Weak transcription	NH-A	brain
12	chr12:29443400-29460200	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr12:29446200-29465000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr12:29448800-29456400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:29449600-29470800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr12:29452000-29457800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr12:29452800-29465200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr12:29452800-29494200	Weak transcription	Lung	lung
19	chr12:29453000-29465200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:29453000-29472800	Weak transcription	Fetal Intestine Large	intestine
21	chr12:29453200-29461800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:29453800-29480000	Weak transcription	Gastric	stomach
23	chr12:29454400-29463800	Weak transcription	HUVEC	blood vessel
24	chr12:29454600-29475800	Weak transcription	Spleen	Spleen
25	chr12:29455200-29489400	Weak transcription	Primary B cells from cord blood	blood
26	chr12:29455400-29458000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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