Variant report

Variant	rs1977552
Chromosome Location	chr9:72059114-72059115
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10867730	0.82[MEX][hapmap]
rs1105307	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11138902	0.81[JPT][hapmap]
rs11138947	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11139063	0.82[MEX][hapmap]
rs11139084	0.82[MEX][hapmap]
rs11139245	0.83[JPT][hapmap]
rs11139246	0.83[JPT][hapmap]
rs11139269	0.82[MEX][hapmap]
rs11793760	0.94[EUR][1000 genomes]
rs12378318	0.85[JPT][hapmap]
rs13290847	0.82[JPT][hapmap]
rs13291679	0.85[JPT][hapmap]
rs13296504	0.87[JPT][hapmap]
rs13297121	0.81[JPT][hapmap]
rs1475641	0.82[JPT][hapmap]
rs1757956	0.88[ASN][1000 genomes]
rs1757960	0.87[ASN][1000 genomes]
rs1761292	0.89[ASN][1000 genomes]
rs1806631	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1831555	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2253778	0.87[JPT][hapmap]
rs2297420	0.81[JPT][hapmap]
rs2309480	0.87[ASN][1000 genomes]
rs2777867	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2781530	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2781531	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2781542	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2991690	0.82[ASN][1000 genomes]
rs2991692	0.90[ASN][1000 genomes]
rs2991693	0.89[ASN][1000 genomes]
rs4307408	0.83[JPT][hapmap]
rs4351475	0.83[JPT][hapmap]
rs4744893	0.87[JPT][hapmap]
rs4744897	0.90[ASN][1000 genomes]
rs4744908	0.82[MEX][hapmap]
rs7019109	0.82[MEX][hapmap]
rs7028920	0.87[JPT][hapmap]
rs7033137	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7851858	0.82[MEX][hapmap]
rs7856029	0.88[ASN][1000 genomes]
rs7869375	0.87[ASN][1000 genomes]
rs867365	0.87[JPT][hapmap]
rs867366	0.87[JPT][hapmap]
rs928563	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9775451	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1048650	chr9:72028458-72179847	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1048256	chr9:72032381-72067786	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1045239	chr9:72032381-72067942	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1041436	chr9:72032381-72069314	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1052872	chr9:72040184-72081554	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1037109	chr9:72040184-72120270	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1039966	chr9:72057304-72181564	Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72036600-72082600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:72041200-72069600	Weak transcription	Gastric	stomach
3	chr9:72042000-72070400	Weak transcription	Spleen	Spleen
4	chr9:72042800-72063800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:72043200-72063800	Weak transcription	Brain Substantia Nigra	brain
6	chr9:72044200-72084400	Weak transcription	Fetal Intestine Small	intestine
7	chr9:72045000-72084400	Weak transcription	Fetal Intestine Large	intestine
8	chr9:72045800-72064200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr9:72046400-72085600	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:72047000-72081800	Weak transcription	Fetal Kidney	kidney
11	chr9:72048000-72068600	Weak transcription	Left Ventricle	heart
12	chr9:72054000-72073200	Weak transcription	Right Ventricle	heart
13	chr9:72055200-72073000	Strong transcription	Liver	Liver
14	chr9:72055400-72059400	Strong transcription	Fetal Brain Female	brain
15	chr9:72055400-72059600	Strong transcription	Ovary	ovary
16	chr9:72055600-72064000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:72056000-72082600	Weak transcription	Pancreas	Pancrea
18	chr9:72056200-72063000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr9:72056400-72061600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:72056400-72080800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr9:72056600-72060400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr9:72056600-72060600	Weak transcription	Primary T cells from cord blood	blood
23	chr9:72056600-72061000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr9:72056600-72062400	Weak transcription	Brain Angular Gyrus	brain
25	chr9:72057000-72061600	Weak transcription	Fetal Thymus	thymus
26	chr9:72057200-72060600	Weak transcription	Fetal Brain Male	brain
27	chr9:72057200-72061600	Weak transcription	Aorta	Aorta
28	chr9:72057200-72061800	Weak transcription	Brain Hippocampus Middle	brain
29	chr9:72057200-72063600	Weak transcription	Brain Anterior Caudate	brain
30	chr9:72057200-72063600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr9:72057200-72063600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr9:72057400-72059400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:72057400-72060000	Enhancers	NHDF-Ad	bronchial
34	chr9:72057400-72061200	Weak transcription	Brain Germinal Matrix	brain
35	chr9:72057400-72061400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr9:72057400-72062200	Weak transcription	Fetal Stomach	stomach
37	chr9:72057400-72063400	Weak transcription	Adipose Nuclei	Adipose
38	chr9:72057800-72059400	Enhancers	NH-A	brain
39	chr9:72058000-72059600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr9:72058200-72080200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr9:72058400-72059800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:72058400-72059800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:72058400-72070600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr9:72058600-72059600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr9:72058800-72059400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:72058800-72059400	Enhancers	HSMMtube	muscle
47	chr9:72058800-72059600	Enhancers	Osteobl	bone
48	chr9:72058800-72061200	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr9:72059000-72059200	Enhancers	Fetal Muscle Leg	muscle
50	chr9:72059000-72059200	Enhancers	HSMM	muscle

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