Variant report

Variant	rs2497681
Chromosome Location	chr10:116397426-116397427
allele	A/C
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: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10885587	0.89[CEU][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10885588	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10885591	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10885592	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10885593	0.88[EUR][1000 genomes]
rs11196805	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs11196811	0.89[CEU][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11196812	0.89[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11196815	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11196817	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11196818	0.89[CEU][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11196820	0.89[CEU][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11196829	0.88[CEU][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11196831	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11196832	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11196833	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11196834	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11196836	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11196838	0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11196839	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11196842	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11196846	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12161653	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12219039	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12571734	0.89[CEU][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12572646	0.91[EUR][1000 genomes]
rs12573191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333689	0.80[CEU][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs17092202	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17092207	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17092213	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17092218	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17092220	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17092237	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2497668	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs2497682	1.00[CEU][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4447090	0.88[CEU][hapmap];0.88[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2497681	SLC18A2	cis	cerebellum	SCAN

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	chr10:116394400-116422600	Weak transcription	Fetal Intestine Small	intestine
5	chr10:116395000-116398200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr10:116395200-116398200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr10:116395200-116398400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr10:116395200-116398400	Weak transcription	A549	lung
9	chr10:116395200-116398600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:116395200-116398800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr10:116395200-116399000	Weak transcription	HUVEC	blood vessel
12	chr10:116395200-116402000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr10:116395400-116397800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr10:116395400-116397800	Weak transcription	HMEC	breast
15	chr10:116395400-116398000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:116395400-116398200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr10:116395400-116398200	Weak transcription	NHLF	lung
18	chr10:116395400-116398400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr10:116395400-116398400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:116395400-116398400	Enhancers	HSMMtube	muscle
21	chr10:116395400-116399000	Weak transcription	Brain Anterior Caudate	brain
22	chr10:116395800-116398000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:116395800-116398000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr10:116395800-116398200	Weak transcription	NHDF-Ad	bronchial
25	chr10:116395800-116398600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr10:116395800-116408400	Weak transcription	Psoas Muscle	Psoas
27	chr10:116396000-116397600	Weak transcription	HSMM	muscle
28	chr10:116396000-116398200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:116396000-116398400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr10:116396000-116401400	Weak transcription	Lung	lung
31	chr10:116396000-116402600	Weak transcription	Adipose Nuclei	Adipose
32	chr10:116396200-116398200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr10:116396200-116398200	Weak transcription	Brain Angular Gyrus	brain
34	chr10:116396200-116398600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr10:116396200-116399000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr10:116396200-116400000	Enhancers	Fetal Heart	heart
37	chr10:116396200-116404400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr10:116396200-116404600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr10:116396200-116408800	Weak transcription	Esophagus	oesophagus
40	chr10:116396400-116397800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr10:116396400-116398200	Weak transcription	Right Ventricle	heart
42	chr10:116396400-116398600	Weak transcription	Brain Hippocampus Middle	brain
43	chr10:116396600-116399000	Weak transcription	Brain Substantia Nigra	brain
44	chr10:116396600-116399600	Weak transcription	Spleen	Spleen
45	chr10:116396600-116404600	Weak transcription	Pancreas	Pancrea
46	chr10:116396800-116398200	Weak transcription	Right Atrium	heart
47	chr10:116397000-116398200	Weak transcription	Left Ventricle	heart
48	chr10:116397200-116399600	Enhancers	Fetal Lung	lung
49	chr10:116397200-116409400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr10:116397400-116398200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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