Variant report

Variant	rs10960813
Chromosome Location	chr9:12819499-12819500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:12817203..12820022-chr9:12879979..12881998,2	MCF-7	breast:
2	chr9:12816711..12819917-chr9:12821131..12823680,3	MCF-7	breast:
3	chr9:12774109..12791345-chr9:12812800..12822770,37	MCF-7	breast:
4	chr9:12773974..12784053-chr9:12813051..12820453,19	MCF-7	breast:
5	chr9:12816957..12819670-chr9:12821766..12823551,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153714	Chromatin interaction

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

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

rs_ID	r²[population]
rs10122949	0.85[EUR][1000 genomes]
rs10960800	0.86[EUR][1000 genomes]
rs10960803	0.83[EUR][1000 genomes]
rs10960804	0.83[EUR][1000 genomes]
rs10960805	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10960806	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10960807	0.84[ASN][1000 genomes]
rs10960808	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10960812	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1318454	0.86[EUR][1000 genomes]
rs34919266	0.83[EUR][1000 genomes]
rs4397503	0.81[EUR][1000 genomes]
rs6474732	0.90[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6474733	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6474736	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs71507332	0.86[EUR][1000 genomes]
rs7846724	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7859336	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9298684	0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12809200-12821400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:12814600-12824800	Weak transcription	Psoas Muscle	Psoas
3	chr9:12814800-12823200	Weak transcription	Colonic Mucosa	Colon
4	chr9:12815000-12819800	Enhancers	Fetal Intestine Small	intestine
5	chr9:12815200-12819600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:12815200-12819800	Enhancers	Fetal Intestine Large	intestine
7	chr9:12815200-12820200	Enhancers	NHLF	lung
8	chr9:12815200-12821400	Enhancers	Osteobl	bone
9	chr9:12815200-12822400	Weak transcription	Brain Angular Gyrus	brain
10	chr9:12815800-12821600	Weak transcription	HSMM	muscle
11	chr9:12816200-12832000	Weak transcription	HSMMtube	muscle
12	chr9:12816600-12819600	Enhancers	Hela-S3	cervix
13	chr9:12817000-12820200	Enhancers	NHDF-Ad	bronchial
14	chr9:12817400-12819600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:12817400-12819800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr9:12817600-12820000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr9:12817800-12819600	Enhancers	NH-A	brain
18	chr9:12818000-12821200	Weak transcription	Fetal Muscle Leg	muscle
19	chr9:12818000-12821400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:12818000-12825000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr9:12818000-12828800	Weak transcription	NHEK	skin
22	chr9:12818600-12820200	Enhancers	HepG2	liver
23	chr9:12818800-12821400	Weak transcription	Lung	lung
24	chr9:12818800-12821400	Weak transcription	Pancreas	Pancrea
25	chr9:12818800-12821400	Weak transcription	Spleen	Spleen
26	chr9:12818800-12822800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:12818800-12826000	Weak transcription	Gastric	stomach
28	chr9:12819000-12819600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:12819000-12819600	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr9:12819000-12820200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr9:12819000-12821400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:12819000-12825600	Weak transcription	Aorta	Aorta
33	chr9:12819200-12820000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:12819200-12820000	Weak transcription	Fetal Lung	lung
35	chr9:12819200-12820000	Weak transcription	Fetal Stomach	stomach
36	chr9:12819200-12820200	Enhancers	A549	lung
37	chr9:12819200-12821000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:12819200-12821400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:12819200-12822400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr9:12819200-12823200	Weak transcription	Fetal Kidney	kidney
41	chr9:12819200-12825000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr9:12819200-12825600	Weak transcription	Liver	Liver
43	chr9:12819200-12826400	Weak transcription	Colon Smooth Muscle	Colon
44	chr9:12819200-12826400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr9:12819200-12826400	Weak transcription	Small Intestine	intestine
46	chr9:12819200-12827600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr9:12819400-12819600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:12819400-12820200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr9:12819400-12821600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr9:12819400-12825200	Weak transcription	Adipose Nuclei	Adipose

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