Variant report

Variant	rs11742324
Chromosome Location	chr5:9059996-9059997
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11134348	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739474	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11954862	0.89[ASN][1000 genomes]
rs12516982	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12520615	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521925	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1354570	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881875	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881898	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881901	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881912	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881913	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881928	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881943	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1902809	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947584	0.89[ASN][1000 genomes]
rs2290735	1.00[CHD][hapmap];0.95[GIH][hapmap]
rs2388001	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2388004	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2388005	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36195254	0.85[EUR][1000 genomes]
rs6871654	0.83[EUR][1000 genomes]
rs6889183	0.89[ASN][1000 genomes]
rs7727526	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv461944	chr5:8758041-9209831	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv597069	chr5:8758041-9209831	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1016937	chr5:8824417-9402871	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv537638	chr5:8824417-9402871	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv918004	chr5:8824417-9402871	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
8	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9038800-9063600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr5:9040200-9064600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:9040800-9122000	Weak transcription	Colonic Mucosa	Colon
4	chr5:9042200-9066600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:9044800-9061400	Weak transcription	Aorta	Aorta
6	chr5:9044800-9065200	Weak transcription	Pancreas	Pancrea
7	chr5:9046600-9065400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:9050000-9065200	Weak transcription	Right Ventricle	heart
9	chr5:9051000-9065200	Weak transcription	Left Ventricle	heart
10	chr5:9051800-9065200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:9053200-9067400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr5:9053400-9060000	Weak transcription	Ovary	ovary
13	chr5:9053800-9077800	Weak transcription	Fetal Heart	heart
14	chr5:9054000-9060200	Weak transcription	Liver	Liver
15	chr5:9054000-9061200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr5:9054400-9060400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr5:9054400-9060600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:9054400-9062600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr5:9054600-9061800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr5:9054600-9062600	Weak transcription	Esophagus	oesophagus
21	chr5:9055000-9060400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:9055200-9061400	Enhancers	NHLF	lung
23	chr5:9055600-9060600	Weak transcription	Fetal Stomach	stomach
24	chr5:9056400-9069000	Weak transcription	Lung	lung
25	chr5:9056800-9060200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:9056800-9061600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:9057000-9061000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:9057200-9060200	Enhancers	Fetal Lung	lung
29	chr5:9057200-9060800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:9057200-9069200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr5:9057400-9060800	Enhancers	NHEK	skin
32	chr5:9057400-9061400	Enhancers	NHDF-Ad	bronchial
33	chr5:9057600-9060800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:9057600-9061000	Enhancers	Muscle Satellite Cultured Cells	--
35	chr5:9057600-9061000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:9057600-9061000	Enhancers	HMEC	breast
37	chr5:9057800-9061000	Enhancers	NH-A	brain
38	chr5:9057800-9061200	Enhancers	Osteobl	bone
39	chr5:9057800-9061400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:9057800-9061400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:9058000-9060400	Weak transcription	Fetal Intestine Small	intestine
42	chr5:9058000-9061400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:9058200-9060400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr5:9058200-9062400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr5:9058400-9060800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:9058600-9060000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr5:9058800-9060800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:9058800-9061400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:9058800-9061600	Enhancers	Fetal Muscle Leg	muscle
50	chr5:9059200-9060000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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