Variant report

Variant	rs10964447
Chromosome Location	chr9:2022988-2022989
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2016219..2019918-chr9:2022215..2026324,5	MCF-7	breast:
2	chr9:2019942..2022254-chr9:2022481..2024574,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000080503	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10757122	0.86[CHB][hapmap]
rs10964457	1.00[YRI][hapmap]
rs10964461	1.00[YRI][hapmap]
rs10964465	0.83[CHD][hapmap]
rs10964466	0.86[CHD][hapmap]
rs10964471	0.83[CHD][hapmap];0.88[TSI][hapmap]
rs10964502	0.84[GIH][hapmap];0.88[TSI][hapmap]
rs72687569	0.89[ASN][1000 genomes]
rs72687570	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs72687571	0.94[ASN][1000 genomes]
rs72687572	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016148	chr9:1457605-2361750	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv539916	chr9:1457605-2361750	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1021712	chr9:1647840-2216839	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv539921	chr9:1647840-2216839	Bivalent Enhancer Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv831493	chr9:1885733-2074135	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv892048	chr9:1888703-2177391	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1021158	chr9:1963930-2040728	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv892052	chr9:1980819-2072470	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	esv2830420	chr9:1998911-2119702	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv613079	chr9:2012767-2059341	Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv466069	chr9:2018825-2066493	Strong transcription Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv613080	chr9:2018825-2066493	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2018000-2028200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:2018200-2023200	Weak transcription	Spleen	Spleen
3	chr9:2018200-2033400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:2018400-2023000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:2018400-2023000	Weak transcription	Gastric	stomach
6	chr9:2018400-2027200	Weak transcription	Esophagus	oesophagus
7	chr9:2018600-2023200	Weak transcription	Pancreas	Pancrea
8	chr9:2019000-2032800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:2019000-2033200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:2019200-2023200	Weak transcription	Aorta	Aorta
11	chr9:2019200-2024600	Weak transcription	HSMMtube	muscle
12	chr9:2019200-2032600	Weak transcription	A549	lung
13	chr9:2019200-2039400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:2019400-2023000	Weak transcription	Fetal Muscle Leg	muscle
15	chr9:2019400-2024600	Weak transcription	Hela-S3	cervix
16	chr9:2019400-2025000	Weak transcription	Colonic Mucosa	Colon
17	chr9:2019400-2025400	Weak transcription	HepG2	liver
18	chr9:2019400-2025800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr9:2019400-2027600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:2019400-2030000	Enhancers	Adipose Nuclei	Adipose
21	chr9:2019400-2030400	Enhancers	Colon Smooth Muscle	Colon
22	chr9:2019400-2030800	Weak transcription	NHDF-Ad	bronchial
23	chr9:2019400-2032800	Weak transcription	Osteobl	bone
24	chr9:2019400-2033000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:2019400-2033200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:2019600-2023000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr9:2019600-2023000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr9:2019600-2023200	Weak transcription	Fetal Stomach	stomach
29	chr9:2019600-2023600	Enhancers	Dnd41	blood
30	chr9:2019800-2023000	Weak transcription	Fetal Brain Female	brain
31	chr9:2019800-2026400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr9:2020000-2023000	Weak transcription	Right Atrium	heart
33	chr9:2020000-2024200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr9:2020000-2024600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr9:2020000-2024800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr9:2020000-2033000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:2020200-2023000	Weak transcription	Brain Germinal Matrix	brain
38	chr9:2020200-2023200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr9:2020200-2023200	Weak transcription	Fetal Intestine Large	intestine
40	chr9:2020200-2023200	Weak transcription	Fetal Intestine Small	intestine
41	chr9:2020200-2024000	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr9:2020200-2024600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:2020400-2023200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:2020400-2023400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr9:2020400-2024400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:2020400-2028800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:2020600-2023000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr9:2021000-2023000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr9:2021200-2026200	Enhancers	Brain Cingulate Gyrus	brain
50	chr9:2021400-2023000	Enhancers	Skeletal Muscle Female	skeletal muscle

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