Variant report

Variant	rs10960808
Chromosome Location	chr9:12815745-12815746
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr9:12815510-12816274	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr9:12814029-12816382	IMR90	lung:	n/a	n/a
3	STAT3	chr9:12815654-12815783	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr9:12815727-12816525	A549	lung:	n/a	chr9:12816066-12816075 chr9:12816066-12816075
5	POLR2A	chr9:12813976-12816199	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr9:12815705-12816474	Hela-S3	cervix:	n/a	chr9:12816066-12816075 chr9:12816066-12816075
7	GATA3	chr9:12815640-12815800	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:12774109..12791345-chr9:12812800..12822770,37	MCF-7	breast:
2	chr9:12773974..12784053-chr9:12813051..12820453,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235448	TF binding region
ENSG00000153714	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10122949	0.83[EUR][1000 genomes]
rs10960800	0.84[EUR][1000 genomes]
rs10960803	0.88[EUR][1000 genomes]
rs10960804	0.88[EUR][1000 genomes]
rs10960805	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10960806	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10960807	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10960812	0.86[ASN][1000 genomes]
rs10960813	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1318454	0.84[EUR][1000 genomes]
rs34919266	0.88[EUR][1000 genomes]
rs4397503	0.88[EUR][1000 genomes]
rs6474732	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6474733	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6474736	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs71507332	0.84[EUR][1000 genomes]
rs7846724	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7859336	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9298684	0.88[EUR][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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12792000-12817200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:12808600-12818400	Weak transcription	Fetal Brain Male	brain
3	chr9:12809200-12817200	Weak transcription	Small Intestine	intestine
4	chr9:12809200-12821400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:12810400-12817600	Weak transcription	Gastric	stomach
6	chr9:12812200-12816200	Enhancers	Fetal Lung	lung
7	chr9:12812200-12816400	Weak transcription	Pancreas	Pancrea
8	chr9:12813600-12816200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr9:12814000-12815800	Enhancers	HSMM	muscle
10	chr9:12814400-12816200	Enhancers	HSMMtube	muscle
11	chr9:12814400-12816800	Enhancers	NHDF-Ad	bronchial
12	chr9:12814400-12818800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr9:12814600-12817400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:12814600-12817600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr9:12814600-12819200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:12814600-12824800	Weak transcription	Psoas Muscle	Psoas
17	chr9:12814800-12817600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr9:12814800-12823200	Weak transcription	Colonic Mucosa	Colon
19	chr9:12815000-12815800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:12815000-12816000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:12815000-12816200	Enhancers	Fetal Kidney	kidney
22	chr9:12815000-12816800	Enhancers	HepG2	liver
23	chr9:12815000-12817600	Weak transcription	Brain Substantia Nigra	brain
24	chr9:12815000-12817800	Weak transcription	Aorta	Aorta
25	chr9:12815000-12817800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr9:12815000-12818200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr9:12815000-12818800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr9:12815000-12819200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr9:12815000-12819800	Enhancers	Fetal Intestine Small	intestine
30	chr9:12815200-12815800	Enhancers	HUVEC	blood vessel
31	chr9:12815200-12815800	Enhancers	NHEK	skin
32	chr9:12815200-12816000	Enhancers	NH-A	brain
33	chr9:12815200-12816200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr9:12815200-12816200	Weak transcription	Stomach Mucosa	stomach
35	chr9:12815200-12816200	Enhancers	Hela-S3	cervix
36	chr9:12815200-12816400	Weak transcription	Liver	Liver
37	chr9:12815200-12817000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr9:12815200-12817200	Weak transcription	Brain Hippocampus Middle	brain
39	chr9:12815200-12817600	Weak transcription	Brain Anterior Caudate	brain
40	chr9:12815200-12817600	Enhancers	Rectal Smooth Muscle	rectum
41	chr9:12815200-12817800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:12815200-12818200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:12815200-12818200	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr9:12815200-12818200	Weak transcription	Fetal Stomach	stomach
45	chr9:12815200-12819200	Enhancers	Colon Smooth Muscle	Colon
46	chr9:12815200-12819200	Enhancers	HMEC	breast
47	chr9:12815200-12819600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:12815200-12819800	Enhancers	Fetal Intestine Large	intestine
49	chr9:12815200-12820200	Enhancers	NHLF	lung
50	chr9:12815200-12821400	Enhancers	Osteobl	bone

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