Variant report

Variant	rs12146316
Chromosome Location	chr10:116396904-116396905
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116395685..116397875-chr10:116401409..116403061,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10444096	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10444097	0.89[ASN][1000 genomes]
rs10787539	0.88[JPT][hapmap]
rs10787540	0.86[JPT][hapmap]
rs11196798	0.86[JPT][hapmap]
rs11196802	0.86[JPT][hapmap]
rs11196804	0.85[ASN][1000 genomes]
rs11196806	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11196810	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11196813	0.89[ASN][1000 genomes]
rs11196814	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11196825	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196826	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196841	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11196844	0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs11196845	0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs11196853	0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs11196854	0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11196856	0.92[ASN][1000 genomes]
rs11196858	0.92[ASN][1000 genomes]
rs11196859	0.91[ASN][1000 genomes]
rs11196861	0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs12359503	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12360417	0.87[ASN][1000 genomes]
rs12763337	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12768716	0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12772864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34811081	0.89[ASN][1000 genomes]
rs4237504	0.89[ASN][1000 genomes]
rs4751620	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4752039	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4752040	0.87[ASN][1000 genomes]
rs4752044	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4752047	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4752071	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4752089	0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs7080854	0.86[JPT][hapmap]
rs7094673	0.86[JPT][hapmap]
rs7907371	0.91[ASN][1000 genomes]
rs955634	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 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	chr10:116392800-116399000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:116393600-116398200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr10:116393600-116405800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr10:116393800-116397200	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr10:116394400-116422600	Weak transcription	Fetal Intestine Small	intestine
6	chr10:116395000-116397000	Enhancers	Left Ventricle	heart
7	chr10:116395000-116398200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr10:116395200-116398200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr10:116395200-116398400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr10:116395200-116398400	Weak transcription	A549	lung
11	chr10:116395200-116398600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr10:116395200-116398800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr10:116395200-116399000	Weak transcription	HUVEC	blood vessel
14	chr10:116395200-116402000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr10:116395400-116397200	Weak transcription	Fetal Lung	lung
16	chr10:116395400-116397800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr10:116395400-116397800	Weak transcription	HMEC	breast
18	chr10:116395400-116398000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr10:116395400-116398200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr10:116395400-116398200	Weak transcription	NHLF	lung
21	chr10:116395400-116398400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr10:116395400-116398400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr10:116395400-116398400	Enhancers	HSMMtube	muscle
24	chr10:116395400-116399000	Weak transcription	Brain Anterior Caudate	brain
25	chr10:116395800-116398000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr10:116395800-116398000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr10:116395800-116398200	Weak transcription	NHDF-Ad	bronchial
28	chr10:116395800-116398600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr10:116395800-116408400	Weak transcription	Psoas Muscle	Psoas
30	chr10:116396000-116397400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr10:116396000-116397600	Weak transcription	HSMM	muscle
32	chr10:116396000-116398200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr10:116396000-116398400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr10:116396000-116401400	Weak transcription	Lung	lung
35	chr10:116396000-116402600	Weak transcription	Adipose Nuclei	Adipose
36	chr10:116396200-116398200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr10:116396200-116398200	Weak transcription	Brain Angular Gyrus	brain
38	chr10:116396200-116398600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr10:116396200-116399000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr10:116396200-116400000	Enhancers	Fetal Heart	heart
41	chr10:116396200-116404400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr10:116396200-116404600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr10:116396200-116408800	Weak transcription	Esophagus	oesophagus
44	chr10:116396400-116397800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr10:116396400-116398200	Weak transcription	Right Ventricle	heart
46	chr10:116396400-116398600	Weak transcription	Brain Hippocampus Middle	brain
47	chr10:116396600-116399000	Weak transcription	Brain Substantia Nigra	brain
48	chr10:116396600-116399600	Weak transcription	Spleen	Spleen
49	chr10:116396600-116404600	Weak transcription	Pancreas	Pancrea
50	chr10:116396800-116397400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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