Variant report

Variant	rs1776209
Chromosome Location	chr10:93810872-93810873
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	chr10:93809868..93812362-chr10:93812392..93814570,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10786029	1.00[YRI][hapmap]
rs11186755	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11186768	0.86[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs1137825	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs11598321	0.86[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap]
rs1229578	1.00[YRI][hapmap]
rs12413858	0.88[JPT][hapmap]
rs12415793	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs12416560	0.86[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs12571564	0.86[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs12763600	0.86[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs12774665	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs1340421	0.86[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs1437	0.86[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1474051	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1622656	1.00[YRI][hapmap]
rs1711846	0.80[ASN][1000 genomes]
rs1776210	0.80[ASN][1000 genomes]
rs2676817	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2676819	0.86[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs2676820	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2676822	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2676825	0.86[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap]
rs2792022	0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2797639	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs3814640	0.85[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap]
rs4375360	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4933224	0.86[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs4933705	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs4933707	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7904126	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7920520	1.00[YRI][hapmap]
rs833367	0.86[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs833372	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs833373	0.80[ASN][1000 genomes]
rs833374	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs833375	0.80[ASN][1000 genomes]
rs833378	0.84[AMR][1000 genomes]
rs833384	0.81[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs855563	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051226	chr10:93711296-93915586	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv540745	chr10:93711296-93915586	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1042818	chr10:93715483-93855032	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv895893	chr10:93747260-93875264	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv551923	chr10:93804974-93835969	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1776209	TNKS2	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93787200-93812200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr10:93787400-93811200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:93787400-93818400	Weak transcription	Colonic Mucosa	Colon
4	chr10:93787400-93840000	Weak transcription	Small Intestine	intestine
5	chr10:93787600-93828000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr10:93788000-93812000	Weak transcription	Brain Anterior Caudate	brain
7	chr10:93788400-93814200	Weak transcription	HepG2	liver
8	chr10:93789800-93816400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr10:93791800-93838400	Weak transcription	Brain Substantia Nigra	brain
10	chr10:93792400-93814800	Weak transcription	Hela-S3	cervix
11	chr10:93792800-93837800	Weak transcription	Brain Angular Gyrus	brain
12	chr10:93793000-93814600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr10:93793200-93812000	Weak transcription	Brain Hippocampus Middle	brain
14	chr10:93793200-93812400	Weak transcription	Placenta	Placenta
15	chr10:93793800-93811400	Weak transcription	Ovary	ovary
16	chr10:93794200-93811400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr10:93794200-93811400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr10:93794200-93811600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr10:93794400-93812400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr10:93794400-93814200	Weak transcription	Osteobl	bone
21	chr10:93794400-93837200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr10:93794800-93811600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr10:93795400-93811600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr10:93795800-93824200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr10:93796200-93840800	Weak transcription	Psoas Muscle	Psoas
26	chr10:93799200-93824000	Weak transcription	HSMMtube	muscle
27	chr10:93805600-93817200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr10:93806000-93811600	Weak transcription	Fetal Stomach	stomach
29	chr10:93806000-93811800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr10:93806000-93811800	Weak transcription	Fetal Intestine Small	intestine
31	chr10:93806000-93817600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr10:93806000-93819400	Weak transcription	Brain Germinal Matrix	brain
33	chr10:93807000-93812800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr10:93807800-93811400	Weak transcription	Adipose Nuclei	Adipose
35	chr10:93808000-93811800	Weak transcription	Aorta	Aorta
36	chr10:93808000-93811800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr10:93808000-93812400	Weak transcription	Lung	lung
38	chr10:93808000-93812600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr10:93808000-93814600	Weak transcription	Primary B cells from cord blood	blood
40	chr10:93808000-93816600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr10:93808000-93817000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr10:93808000-93820000	Weak transcription	Fetal Brain Female	brain
43	chr10:93808000-93825400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr10:93808000-93825600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr10:93808000-93842600	Weak transcription	Fetal Lung	lung
46	chr10:93808200-93811400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr10:93808200-93811600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr10:93808200-93811800	Weak transcription	Spleen	Spleen
49	chr10:93808200-93812000	Weak transcription	Pancreas	Pancrea
50	chr10:93808200-93812400	Weak transcription	Thymus	Thymus

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