Variant report

Variant	rs2715609
Chromosome Location	chr3:133549938-133549939
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:133540918..133542812-chr3:133549645..133551842,2	MCF-7	breast:
2	chr3:133544073..133548736-chr3:133549293..133553405,5	K562	blood:
3	chr3:133543993..133545850-chr3:133548692..133550579,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1043147	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11710936	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12637730	0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16840994	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16841004	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2249322	0.83[CEU][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2293373	0.84[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2293374	0.84[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2293375	0.95[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2692667	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2692668	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692670	0.84[CEU][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2692671	0.80[ASN][1000 genomes]
rs2715607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2715608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3811659	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7626433	0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.98[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	nsv877506	chr3:133423473-133569777	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS 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 miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2715609	SRPRB	Cis_1M	lymphoblastoid	RTeQTL
rs2715609	SRPRB	cis	multi-tissue	Pritchard

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133539400-133572200	Weak transcription	Fetal Brain Male	brain
2	chr3:133541000-133551000	Weak transcription	Brain Angular Gyrus	brain
3	chr3:133541400-133558200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:133541400-133559600	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:133542000-133555400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:133542000-133563600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:133542600-133557800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:133542800-133569000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:133543000-133553600	Weak transcription	Fetal Lung	lung
10	chr3:133543400-133560600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:133543600-133550400	Weak transcription	Thymus	Thymus
12	chr3:133543800-133550800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:133543800-133552400	Weak transcription	Placenta	Placenta
14	chr3:133543800-133554000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:133543800-133560000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:133544000-133550600	Weak transcription	Brain Substantia Nigra	brain
17	chr3:133544000-133556600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:133544200-133551600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:133544200-133551600	Weak transcription	Aorta	Aorta
20	chr3:133544200-133557600	Weak transcription	Adipose Nuclei	Adipose
21	chr3:133544400-133559800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:133544600-133562200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:133544600-133573200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:133544600-133584200	Weak transcription	Esophagus	oesophagus
25	chr3:133545000-133582800	Weak transcription	Gastric	stomach
26	chr3:133545200-133550400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:133545200-133552400	Weak transcription	Spleen	Spleen
28	chr3:133545200-133553400	Weak transcription	Pancreas	Pancrea
29	chr3:133545200-133557600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:133545600-133550600	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:133545600-133552600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:133545600-133552600	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:133546000-133552000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:133546200-133550200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:133546200-133550800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr3:133546200-133551600	Weak transcription	Fetal Stomach	stomach
37	chr3:133546200-133557400	Weak transcription	Fetal Intestine Small	intestine
38	chr3:133546600-133550800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:133547600-133550000	Enhancers	Fetal Heart	heart
40	chr3:133548000-133559600	Weak transcription	Lung	lung
41	chr3:133548000-133563400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:133548000-133564400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:133548200-133560600	Strong transcription	Brain Germinal Matrix	brain
44	chr3:133548400-133550400	Weak transcription	Fetal Brain Female	brain
45	chr3:133548800-133550000	Enhancers	Right Atrium	heart
46	chr3:133549000-133560000	Strong transcription	Brain Anterior Caudate	brain
47	chr3:133549200-133561200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:133549200-133562400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:133549600-133550600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:133549800-133553000	Weak transcription	Left Ventricle	heart

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