Variant report

Variant	rs3897757
Chromosome Location	chr9:72075130-72075131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1009617	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10511966	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10867682	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs10867768	0.82[JPT][hapmap]
rs11138902	0.96[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11139065	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs11139224	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs11139245	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs11139246	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs11139274	0.82[JPT][hapmap]
rs11139289	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs1228285	0.97[ASN][1000 genomes]
rs1236984	0.92[ASN][1000 genomes]
rs1237679	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12378157	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs12378318	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs12553491	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs13286303	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs13286400	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs13288354	0.81[JPT][hapmap]
rs13289730	0.82[JPT][hapmap]
rs13290847	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs13291679	0.80[JPT][hapmap]
rs13293185	0.81[ASN][1000 genomes]
rs13296504	0.87[JPT][hapmap]
rs13297121	0.81[JPT][hapmap]
rs13302431	0.84[ASN][1000 genomes]
rs1330331	0.82[JPT][hapmap]
rs1331978	0.84[ASN][1000 genomes]
rs1475641	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs1619631	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1631688	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1631780	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1757955	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1757961	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1761284	0.86[ASN][1000 genomes]
rs1761286	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1761287	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1889400	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2253778	0.96[CHB][hapmap];0.96[JPT][hapmap];0.81[ASN][1000 genomes]
rs2297420	0.96[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2777860	0.81[ASN][1000 genomes]
rs2777861	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2777864	0.90[ASN][1000 genomes]
rs2781537	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2781539	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2781540	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2781541	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4307408	0.82[JPT][hapmap]
rs4351475	0.81[JPT][hapmap]
rs4744884	0.86[JPT][hapmap]
rs4744893	0.87[JPT][hapmap]
rs4744898	0.86[ASN][1000 genomes]
rs4744899	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7028920	0.87[JPT][hapmap]
rs867365	0.86[JPT][hapmap]
rs867366	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
6	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
7	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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72036600-72082600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:72044200-72084400	Weak transcription	Fetal Intestine Small	intestine
3	chr9:72045000-72084400	Weak transcription	Fetal Intestine Large	intestine
4	chr9:72046400-72085600	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:72047000-72081800	Weak transcription	Fetal Kidney	kidney
6	chr9:72056000-72082600	Weak transcription	Pancreas	Pancrea
7	chr9:72056400-72080800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:72058200-72080200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr9:72059400-72080200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:72064600-72084200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:72064600-72084200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr9:72064800-72083800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr9:72066200-72081000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:72066400-72075400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr9:72067400-72078800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:72067600-72080800	Weak transcription	NHDF-Ad	bronchial
17	chr9:72067800-72080800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr9:72069000-72080600	Weak transcription	Left Ventricle	heart
19	chr9:72070400-72080000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr9:72070600-72081000	Weak transcription	Brain Substantia Nigra	brain
21	chr9:72070800-72085600	Weak transcription	Gastric	stomach
22	chr9:72071000-72080400	Weak transcription	Fetal Muscle Leg	muscle
23	chr9:72071400-72075200	Weak transcription	Fetal Brain Female	brain
24	chr9:72071400-72076400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:72071400-72076600	Weak transcription	Brain Anterior Caudate	brain
26	chr9:72071400-72078800	Weak transcription	Spleen	Spleen
27	chr9:72071400-72080000	Weak transcription	Adipose Nuclei	Adipose
28	chr9:72071400-72080200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr9:72071400-72080800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:72071600-72079600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr9:72071600-72080400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:72072000-72079600	Weak transcription	Fetal Stomach	stomach
33	chr9:72072000-72080400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr9:72072000-72080600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:72072400-72078400	Weak transcription	Ovary	ovary
36	chr9:72072400-72084000	Weak transcription	Fetal Heart	heart
37	chr9:72072600-72076400	Weak transcription	Aorta	Aorta
38	chr9:72072600-72077000	Weak transcription	Brain Angular Gyrus	brain
39	chr9:72073800-72075200	Strong transcription	Brain Hippocampus Middle	brain
40	chr9:72073800-72078400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr9:72074200-72075200	Strong transcription	Liver	Liver
42	chr9:72074200-72077800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr9:72074200-72078200	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr9:72074400-72075200	Strong transcription	Brain Germinal Matrix	brain
45	chr9:72074600-72075200	Strong transcription	Fetal Lung	lung
46	chr9:72074800-72075600	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr9:72075000-72077200	Enhancers	Fetal Brain Male	brain

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