Variant report

Variant	rs7315346
Chromosome Location	chr12:29411229-29411230
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1006410	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1072724	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10743656	0.92[AFR][1000 genomes]
rs10771514	0.92[AFR][1000 genomes]
rs10843376	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10843385	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11050147	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050149	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11050168	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12301475	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12578931	0.87[ASN][1000 genomes]
rs12581107	0.87[ASN][1000 genomes]
rs17715086	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2016832	0.92[AFR][1000 genomes]
rs2288128	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2288129	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2350315	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3782505	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3782510	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3948497	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4277150	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4931171	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487807	0.92[AFR][1000 genomes]
rs7298031	0.92[AFR][1000 genomes]
rs7299283	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7313552	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7358667	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7956305	0.92[AFR][1000 genomes]
rs7959145	0.92[AFR][1000 genomes]
rs7961943	0.92[AFR][1000 genomes]
rs7964831	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7980218	0.92[AFR][1000 genomes]
rs986072	0.87[EUR][1000 genomes];0.90[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
rs7315346	RP11-996F15.2	cis	lung	GTEx
rs7315346	RP11-996F15.2	cis	Thyroid	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29396800-29413200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr12:29400800-29411400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr12:29408200-29413000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:29408200-29413400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:29408200-29423200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:29408200-29425800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:29408400-29414000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:29408400-29424000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:29408800-29413400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:29409200-29412600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:29409400-29413200	Weak transcription	Fetal Intestine Small	intestine
12	chr12:29410000-29412600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:29410000-29412600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:29410000-29413400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:29410000-29415200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:29410000-29421000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:29410000-29425800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:29410000-29426200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:29410800-29413600	Weak transcription	Rectal Mucosa Donor 29	rectum

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