Variant report

Variant	rs13083246
Chromosome Location	chr3:156248263-156248264
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156244041..156246275-chr3:156247961..156249711,2	MCF-7	breast:
2	chr3:155868593..155869135-chr3:156248238..156248852,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10936027	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710396	0.87[ASN][1000 genomes]
rs12107507	1.00[YRI][hapmap]
rs13065924	0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs13068904	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088140	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs17354147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2874390	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3773717	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3773719	0.96[ASN][1000 genomes]
rs6441074	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs6441075	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs6441076	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs6764265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764992	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771728	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6802811	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71310479	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71310481	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs756335	0.90[CEU][hapmap]
rs7619602	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs8665	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9837799	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9917691	0.96[ASN][1000 genomes]

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	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv829764	chr3:156174824-156347774	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	nsv877683	chr3:156180366-156272351	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13083246	SSR3	cis	lymphoblastoid	seeQTL
rs13083246	SSR3	cis	Liver	GTEx
rs13083246	SSR3	cis	multi-tissue	Pritchard
rs13083246	SSR3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156230200-156251000	Weak transcription	Left Ventricle	heart
2	chr3:156232200-156249200	Weak transcription	Gastric	stomach
3	chr3:156234400-156248600	Weak transcription	Brain Anterior Caudate	brain
4	chr3:156234400-156251200	Weak transcription	Ovary	ovary
5	chr3:156236000-156250200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:156236800-156251000	Weak transcription	Pancreas	Pancrea
7	chr3:156236800-156251200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:156237200-156250600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:156238200-156251400	Weak transcription	A549	lung
10	chr3:156240400-156260200	Weak transcription	Esophagus	oesophagus
11	chr3:156240600-156251800	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:156241600-156250800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:156241600-156255800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:156241800-156251000	Weak transcription	HSMMtube	muscle
15	chr3:156242000-156253000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:156242200-156251200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:156243000-156255200	Weak transcription	Dnd41	blood
18	chr3:156243200-156251000	Weak transcription	HSMM	muscle
19	chr3:156243200-156253800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:156243200-156255600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:156243200-156255600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:156243200-156255800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr3:156243200-156256600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:156243200-156256800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:156243200-156256800	Weak transcription	GM12878-XiMat	blood
26	chr3:156243200-156257000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:156243200-156257000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:156243200-156258800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr3:156243400-156256600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr3:156243400-156256800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:156244000-156249800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:156244000-156257000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:156244200-156250400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:156244400-156253000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:156244600-156248600	Weak transcription	Adipose Nuclei	Adipose
36	chr3:156244600-156257000	Weak transcription	Lung	lung
37	chr3:156244800-156252200	Weak transcription	NHLF	lung
38	chr3:156245000-156257000	Weak transcription	Spleen	Spleen
39	chr3:156245400-156257200	Weak transcription	Fetal Brain Male	brain
40	chr3:156246000-156249400	Enhancers	Brain Hippocampus Middle	brain
41	chr3:156246000-156253200	Weak transcription	Fetal Stomach	stomach
42	chr3:156246200-156249600	Enhancers	Brain Substantia Nigra	brain
43	chr3:156246600-156248600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:156246600-156252800	Weak transcription	Liver	Liver
45	chr3:156246800-156252800	Weak transcription	Fetal Intestine Small	intestine
46	chr3:156246800-156263600	Weak transcription	Fetal Brain Female	brain
47	chr3:156247000-156251200	Weak transcription	Aorta	Aorta
48	chr3:156247200-156253000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:156247200-156263800	Weak transcription	Thymus	Thymus
50	chr3:156247600-156249200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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