Variant report

Variant	rs9682606
Chromosome Location	chr3:140978098-140978099
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	chr3:140975814..140978503-chr3:140979443..140982221,2	MCF-7	breast:
2	chr3:140977766..140980226-chr3:141006718..141009392,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155893	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11556022	1.00[JPT][hapmap]
rs11713226	0.94[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11713257	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16851191	0.94[CEU][hapmap];0.96[YRI][hapmap]
rs4683587	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4683589	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55694384	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57562453	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439989	0.81[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap]
rs6762331	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6794495	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72982520	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72994962	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72994967	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73869553	0.84[ASN][1000 genomes]
rs7618821	0.89[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs7629005	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv877551	chr3:140970556-141029860	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9682606	TRPC1	cis	parietal	SCAN
rs9682606	ACPL2	cis	cerebellum	SCAN
rs9682606	ACPL2	cis	parietal	SCAN
rs9682606	RBP2	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140951600-140979000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:140955200-140980600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr3:140955400-140985800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:140957400-141001000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:140959200-140998400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:140960000-140980000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:140961000-140978800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:140961200-140985800	Weak transcription	Adipose Nuclei	Adipose
9	chr3:140961200-141012600	Weak transcription	Aorta	Aorta
10	chr3:140961400-140983200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:140962000-140985800	Weak transcription	Brain Anterior Caudate	brain
12	chr3:140962400-140979200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:140962600-140978800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:140962600-140979600	Weak transcription	Fetal Intestine Large	intestine
15	chr3:140962600-140980600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:140963400-140982800	Weak transcription	Brain Germinal Matrix	brain
17	chr3:140963600-140978800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:140966000-140990200	Weak transcription	Psoas Muscle	Psoas
19	chr3:140966200-140979600	Weak transcription	Pancreas	Pancrea
20	chr3:140968200-140979000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:140968200-140990000	Weak transcription	Gastric	stomach
22	chr3:140968400-140982800	Weak transcription	Fetal Lung	lung
23	chr3:140971000-140979000	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr3:140972000-140979000	Weak transcription	Fetal Intestine Small	intestine
25	chr3:140972200-140979000	Weak transcription	Fetal Stomach	stomach
26	chr3:140973200-140979000	Enhancers	Fetal Thymus	thymus
27	chr3:140974800-140985800	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:140974800-140987400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:140974800-140991400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:140975000-140979200	Weak transcription	Brain Angular Gyrus	brain
31	chr3:140975000-140979400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:140975000-140979400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:140975000-140979800	Weak transcription	Brain Substantia Nigra	brain
34	chr3:140975000-140984800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:140975000-140985800	Weak transcription	Right Atrium	heart
36	chr3:140975000-140993400	Weak transcription	Lung	lung
37	chr3:140975000-140993400	Weak transcription	Spleen	Spleen
38	chr3:140975200-140980600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:140975200-140984400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:140975200-140984800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:140975200-140985000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:140975200-140991800	Weak transcription	Placenta	Placenta
43	chr3:140975400-140978400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:140975400-140978600	Genic enhancers	Dnd41	blood
45	chr3:140975400-140978800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:140975400-140979000	Weak transcription	Right Ventricle	heart
47	chr3:140975400-140979400	Weak transcription	Left Ventricle	heart
48	chr3:140975400-140979600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr3:140975400-140980000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr3:140975400-140980600	Weak transcription	HSMM	muscle

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