Variant report

Variant	rs1757960
Chromosome Location	chr9:72068699-72068700
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72068242..72070671-chr9:72077608..72079150,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1105307	0.86[ASN][1000 genomes]
rs11138902	0.82[JPT][hapmap]
rs11138947	0.91[JPT][hapmap]
rs11139245	0.83[JPT][hapmap]
rs11139246	0.83[JPT][hapmap]
rs12378318	0.86[JPT][hapmap]
rs13290847	0.82[JPT][hapmap]
rs13291679	0.86[JPT][hapmap]
rs13296504	0.87[JPT][hapmap]
rs13297121	0.82[JPT][hapmap]
rs1475641	0.82[JPT][hapmap]
rs1757956	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1757961	0.80[ASN][1000 genomes]
rs1761292	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1806631	0.87[ASN][1000 genomes]
rs1831555	0.88[ASN][1000 genomes]
rs1977552	0.87[ASN][1000 genomes]
rs2253778	0.87[JPT][hapmap]
rs2297420	0.82[JPT][hapmap]
rs2309480	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2777867	0.88[ASN][1000 genomes]
rs2781530	0.87[ASN][1000 genomes]
rs2781531	0.88[ASN][1000 genomes]
rs2991690	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2991691	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2991692	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2991693	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4307408	0.83[JPT][hapmap]
rs4351475	0.83[JPT][hapmap]
rs4744893	0.87[JPT][hapmap]
rs4744897	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7028920	0.87[JPT][hapmap]
rs7033137	0.82[ASN][1000 genomes]
rs7856029	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7869375	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867365	0.87[JPT][hapmap]
rs867366	0.87[JPT][hapmap]
rs928563	0.90[ASN][1000 genomes]
rs9775451	0.82[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	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	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
6	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
7	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
8	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	chr9:72044200-72084400	Weak transcription	Fetal Intestine Small	intestine
5	chr9:72045000-72084400	Weak transcription	Fetal Intestine Large	intestine
6	chr9:72046400-72085600	Weak transcription	Colon Smooth Muscle	Colon
7	chr9:72047000-72081800	Weak transcription	Fetal Kidney	kidney
8	chr9:72054000-72073200	Weak transcription	Right Ventricle	heart
9	chr9:72055200-72073000	Strong transcription	Liver	Liver
10	chr9:72056000-72082600	Weak transcription	Pancreas	Pancrea
11	chr9:72056400-72080800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:72058200-72080200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr9:72058400-72070600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr9:72059400-72072400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:72059400-72080200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:72059600-72069600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:72061000-72070000	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr9:72061200-72071400	Strong transcription	Brain Germinal Matrix	brain
19	chr9:72062200-72068800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr9:72062200-72070200	Strong transcription	Fetal Stomach	stomach
21	chr9:72062200-72072600	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:72062800-72072400	Strong transcription	Ovary	ovary
23	chr9:72063800-72070000	Strong transcription	Brain Substantia Nigra	brain
24	chr9:72064600-72084200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr9:72064600-72084200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr9:72064800-72069400	Weak transcription	Adipose Nuclei	Adipose
27	chr9:72064800-72071400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr9:72064800-72083800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr9:72065600-72068800	Strong transcription	Brain Angular Gyrus	brain
30	chr9:72065800-72071400	Strong transcription	Fetal Brain Female	brain
31	chr9:72066000-72070000	Strong transcription	Brain Hippocampus Middle	brain
32	chr9:72066200-72071400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:72066200-72081000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:72066400-72075400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:72066800-72075000	Weak transcription	Fetal Brain Male	brain
36	chr9:72067000-72068800	Weak transcription	Brain Anterior Caudate	brain
37	chr9:72067400-72069400	Weak transcription	Aorta	Aorta
38	chr9:72067400-72069600	Weak transcription	Fetal Muscle Leg	muscle
39	chr9:72067400-72069800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr9:72067400-72070000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr9:72067400-72070400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:72067400-72078800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:72067600-72080800	Weak transcription	NHDF-Ad	bronchial
44	chr9:72067800-72080800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr9:72068000-72068800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr9:72068000-72070800	Weak transcription	Fetal Lung	lung
47	chr9:72068200-72068800	Enhancers	Primary T cells from cord blood	blood
48	chr9:72068200-72069800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr9:72068400-72069000	Enhancers	HUVEC	blood vessel
50	chr9:72068400-72069200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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