Variant report

Variant	rs10960806
Chromosome Location	chr9:12812725-12812726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:12796888..12798629-chr9:12811320..12813907,2	MCF-7	breast:
2	chr9:12809497..12811104-chr9:12812287..12814300,2	MCF-7	breast:
3	chr9:12785493..12787579-chr9:12811391..12813312,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10960805	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10960807	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10960808	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10960812	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10960813	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6474732	0.84[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6474733	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6474736	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7846724	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7859336	1.00[JPT][hapmap];0.91[ASN][1000 genomes]

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	nsv869288	chr9:12286919-12816766	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv892575	chr9:12804243-12852462	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12785800-12813600	Weak transcription	Fetal Intestine Large	intestine
2	chr9:12786000-12813600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr9:12786000-12813600	Weak transcription	Fetal Intestine Small	intestine
4	chr9:12792000-12817200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:12795800-12813400	Weak transcription	Fetal Kidney	kidney
6	chr9:12795800-12813800	Weak transcription	Fetal Stomach	stomach
7	chr9:12798600-12812800	Weak transcription	NH-A	brain
8	chr9:12802400-12812800	Weak transcription	HUVEC	blood vessel
9	chr9:12802400-12814000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:12808600-12818400	Weak transcription	Fetal Brain Male	brain
11	chr9:12809200-12814000	Weak transcription	Psoas Muscle	Psoas
12	chr9:12809200-12817200	Weak transcription	Small Intestine	intestine
13	chr9:12809200-12821400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:12809600-12814200	Weak transcription	Brain Hippocampus Middle	brain
15	chr9:12810000-12814000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr9:12810200-12813400	Weak transcription	HepG2	liver
17	chr9:12810200-12813600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr9:12810200-12813800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:12810200-12814000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:12810400-12813600	Weak transcription	Stomach Mucosa	stomach
21	chr9:12810400-12814000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:12810400-12814000	Weak transcription	Aorta	Aorta
23	chr9:12810400-12814000	Weak transcription	Brain Angular Gyrus	brain
24	chr9:12810400-12817600	Weak transcription	Gastric	stomach
25	chr9:12810600-12813800	Weak transcription	Adipose Nuclei	Adipose
26	chr9:12810800-12813800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr9:12811400-12813400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:12811600-12813800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:12812000-12813400	Enhancers	NHDF-Ad	bronchial
30	chr9:12812000-12814000	Enhancers	Colon Smooth Muscle	Colon
31	chr9:12812000-12814000	Weak transcription	HSMMtube	muscle
32	chr9:12812200-12812800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr9:12812200-12813000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:12812200-12813800	Enhancers	Osteobl	bone
35	chr9:12812200-12814400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:12812200-12816200	Enhancers	Fetal Lung	lung
37	chr9:12812200-12816400	Weak transcription	Pancreas	Pancrea
38	chr9:12812400-12812800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr9:12812400-12812800	Flanking Active TSS	NHEK	skin
40	chr9:12812400-12813000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:12812600-12812800	Flanking Active TSS	HMEC	breast
42	chr9:12812600-12812800	Enhancers	NHLF	lung
43	chr9:12812600-12813200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:12812600-12813400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:12812600-12813400	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr9:12812600-12813400	Enhancers	A549	lung
47	chr9:12812600-12813800	Enhancers	Hela-S3	cervix
48	chr9:12812600-12814000	Enhancers	Muscle Satellite Cultured Cells	--
49	chr9:12812600-12814000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr9:12812600-12814000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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