Variant report

Variant	rs7301398
Chromosome Location	chr12:29455390-29455391
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1035604	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10771508	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs10843361	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs10843366	0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.86[ASN][1000 genomes]
rs10843367	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10843371	0.86[ASN][1000 genomes]
rs10843377	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10843382	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10843384	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10843403	0.82[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs11050152	0.81[ASN][1000 genomes]
rs11050157	0.84[ASN][1000 genomes]
rs11050161	0.85[ASN][1000 genomes]
rs11050162	0.85[ASN][1000 genomes]
rs11050167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11050170	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11050173	0.97[ASN][1000 genomes]
rs11050181	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11050187	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11050188	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11050189	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050190	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11050191	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11050192	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11050193	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11050194	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11050208	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12228468	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12231498	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12366505	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12366527	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16934135	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1989478	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1991114	0.80[ASN][1000 genomes]
rs2042511	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs2194518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2194519	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs2194520	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs2216853	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2216854	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs3764953	0.94[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3782506	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3782509	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3782511	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4331146	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57803026	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6487796	0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs6487801	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6487804	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6487805	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487808	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67146951	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67517901	0.86[ASN][1000 genomes]
rs7294598	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7301188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7308125	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs7311912	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7312164	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7316004	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7954278	0.90[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7954871	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7957339	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7973786	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7974221	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7976961	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs918873	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9738721	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7301398	RP11-996F15.2	cis	Adipose Subcutaneous	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	chr12:29453200-29455400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:29453200-29461800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:29453800-29480000	Weak transcription	Gastric	stomach
24	chr12:29454400-29463800	Weak transcription	HUVEC	blood vessel
25	chr12:29454600-29475800	Weak transcription	Spleen	Spleen
26	chr12:29455200-29489400	Weak transcription	Primary B cells from cord blood	blood

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