Variant report

Variant	rs7968883
Chromosome Location	chr12:29394191-29394192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10450679	0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10743651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10743652	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10771512	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10843365	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843372	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10843402	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs1120528	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1991113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2059362	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2194517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2350316	0.82[ASN][1000 genomes]
rs2882294	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782507	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3782508	0.95[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4370971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4412790	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6487789	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487791	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6487792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487795	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6487796	0.83[CEU][hapmap]
rs6487797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6487799	0.85[EUR][1000 genomes]
rs6487800	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6487802	0.95[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6487803	0.95[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7134187	0.95[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7137141	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7295212	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7299648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7299772	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7300032	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7301575	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7302399	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7303960	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73063614	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7308534	0.95[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap]
rs7311081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7315535	0.87[AFR][1000 genomes]
rs7316026	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs766445	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7954375	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954990	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7968167	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7971296	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7972032	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs7974254	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976227	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7976667	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9669514	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9738165	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3431050	chr12:29394152-29394604	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7968883	RP11-996F15.2	cis	lung	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29379600-29394600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:29381800-29394600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:29381800-29394800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:29388600-29394800	Weak transcription	NHEK	skin
5	chr12:29388800-29394600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:29390200-29394800	Enhancers	HUVEC	blood vessel
7	chr12:29390400-29394400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:29391600-29400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:29391800-29394600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:29391800-29400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:29392200-29394600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr12:29392400-29394200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:29392400-29394200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:29392400-29394200	Weak transcription	Adipose Nuclei	Adipose
15	chr12:29392400-29394400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:29392400-29394600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:29392400-29394600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:29392400-29394600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:29392400-29394600	Weak transcription	NH-A	brain
20	chr12:29392400-29395000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr12:29392400-29395400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:29392600-29394400	Weak transcription	Osteobl	bone
23	chr12:29392800-29396000	Enhancers	Placenta	Placenta
24	chr12:29393000-29394400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:29393200-29394400	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr12:29393200-29394600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr12:29393200-29394600	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr12:29393200-29395000	Enhancers	Primary hematopoietic stem cells	blood
29	chr12:29393200-29396000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr12:29393200-29397000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr12:29393400-29394400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:29393400-29394600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:29393400-29394600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr12:29393400-29394600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr12:29393400-29395400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:29393400-29395400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:29393400-29396000	Enhancers	Duodenum Mucosa	Duodenum
38	chr12:29393400-29396600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:29393600-29394600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr12:29393600-29394600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:29393600-29394600	Weak transcription	Fetal Intestine Large	intestine
42	chr12:29393600-29394600	Weak transcription	Fetal Thymus	thymus
43	chr12:29393600-29394600	Weak transcription	Lung	lung
44	chr12:29393600-29394600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:29394000-29395800	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr12:29394000-29395800	Enhancers	Stomach Smooth Muscle	stomach
47	chr12:29394000-29396200	Enhancers	Colonic Mucosa	Colon
48	chr12:29394000-29396200	Enhancers	NHDF-Ad	bronchial

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