Variant report

Variant	rs13081671
Chromosome Location	chr3:135876549-135876550
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	chr3:135871018..135872662-chr3:135874899..135876560,2	MCF-7	breast:
2	chr3:135874998..135877491-chr3:135913896..135916002,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10048942	0.95[CEU][hapmap]
rs10222451	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10512987	1.00[CHD][hapmap]
rs10512990	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12330335	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12695644	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13068210	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13079205	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13082532	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13097248	0.81[CEU][hapmap]
rs13321220	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1393786	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1393787	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1403763	1.00[CEU][hapmap]
rs2305265	1.00[CHB][hapmap]
rs28519617	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28535121	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28669017	1.00[GIH][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34864445	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35320690	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs35352346	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3732519	1.00[CHB][hapmap]
rs3732521	1.00[CHB][hapmap]
rs3821444	1.00[CHB][hapmap]
rs3905668	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56398805	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6439629	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67109185	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67589653	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6767060	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6769762	0.89[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs6771253	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs6775778	0.95[CEU][hapmap];0.83[MEX][hapmap]
rs6786532	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6786582	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6792630	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6793835	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6799056	0.94[CEU][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6799320	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6799503	0.90[ASN][1000 genomes]
rs73222236	0.87[ASN][1000 genomes]
rs73222243	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9653930	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9827662	0.89[CEU][hapmap]
rs9834966	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9837158	0.91[GIH][hapmap]
rs9844666	0.91[GIH][hapmap]
rs9848926	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9870122	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9881400	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][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	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv877518	chr3:135861666-135885554	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv967232	chr3:135871526-135887926	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13081671	PPP2R3A	cis	cerebellum	SCAN
rs13081671	MSL2	cis	cerebellum	SCAN
rs13081671	RNF184	cis	multi-tissue	Pritchard

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135845600-135880400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:135862000-135904800	Weak transcription	Hela-S3	cervix
3	chr3:135864200-135882400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:135864400-135882600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:135864400-135885200	Weak transcription	Brain Germinal Matrix	brain
6	chr3:135865600-135882400	Weak transcription	Fetal Heart	heart
7	chr3:135868800-135883000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:135869800-135882400	Weak transcription	Brain Angular Gyrus	brain
9	chr3:135870400-135881000	Weak transcription	Right Atrium	heart
10	chr3:135870800-135895200	Weak transcription	Fetal Intestine Small	intestine
11	chr3:135871000-135881800	Weak transcription	Right Ventricle	heart
12	chr3:135871000-135882400	Weak transcription	Esophagus	oesophagus
13	chr3:135871000-135882400	Weak transcription	Small Intestine	intestine
14	chr3:135871000-135897600	Weak transcription	Aorta	Aorta
15	chr3:135871200-135882200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:135871200-135905000	Weak transcription	Fetal Stomach	stomach
17	chr3:135871400-135880000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:135871400-135880200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:135871400-135882200	Weak transcription	HUVEC	blood vessel
20	chr3:135871400-135882400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:135871400-135885000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:135871400-135885000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:135871400-135885600	Weak transcription	Fetal Kidney	kidney
24	chr3:135871600-135880000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:135871600-135880400	Weak transcription	Adipose Nuclei	Adipose
26	chr3:135871600-135880800	Weak transcription	Psoas Muscle	Psoas
27	chr3:135871600-135881800	Weak transcription	Brain Substantia Nigra	brain
28	chr3:135871600-135882200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:135871600-135882400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:135871600-135882400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:135871600-135882400	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:135871600-135883000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:135871600-135884800	Weak transcription	K562	blood
34	chr3:135871600-135885000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:135871800-135877000	Enhancers	Primary T cells fromperipheralblood	blood
36	chr3:135871800-135882200	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr3:135872000-135876600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:135872000-135877200	Weak transcription	Primary T cells from cord blood	blood
39	chr3:135872000-135877400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:135872000-135882200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:135872000-135882200	Weak transcription	Primary B cells from cord blood	blood
42	chr3:135872000-135882200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:135872000-135882400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:135872000-135882400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:135872000-135882400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:135872000-135882400	Weak transcription	Fetal Lung	lung
47	chr3:135872000-135885000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr3:135872000-135887800	Weak transcription	HSMM	muscle
49	chr3:135872200-135879800	Weak transcription	GM12878-XiMat	blood
50	chr3:135872200-135880000	Weak transcription	Dnd41	blood

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