Variant report

Variant	rs35352346
Chromosome Location	chr3:135881488-135881489
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:135881085..135883253-chr3:135914338..135916372,2	MCF-7	breast:
2	chr3:135881427..135883402-chr3:135892260..135894929,2	MCF-7	breast:
3	chr3:135879587..135883583-chr3:135913683..135917123,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10048942	0.89[CEU][hapmap]
rs10222451	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10512987	0.89[CHD][hapmap]
rs10512990	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12330335	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12695644	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13068210	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13079205	0.95[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13081671	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]
rs13082532	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13321220	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1393786	0.95[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1393787	0.95[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1403763	0.95[CEU][hapmap]
rs2305265	1.00[CHB][hapmap]
rs28519617	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28535121	0.95[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28669017	1.00[GIH][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34864445	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35320690	0.95[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs3732519	1.00[CHB][hapmap]
rs3732521	1.00[CHB][hapmap]
rs3821444	1.00[CHB][hapmap]
rs3905668	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56398805	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6439629	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67109185	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67589653	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6767060	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6769762	0.89[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs6771253	1.00[CHB][hapmap]
rs6775778	0.89[CEU][hapmap]
rs6786532	1.00[CHB][hapmap]
rs6786582	0.95[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6792630	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6793835	0.95[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6799056	0.89[CEU][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6799320	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73222243	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9653930	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9827662	0.84[CEU][hapmap]
rs9834966	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9837158	0.91[GIH][hapmap]
rs9844666	0.91[GIH][hapmap]
rs9848926	0.95[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9870122	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9881400	0.95[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs35352346	MSL2	cis	cerebellum	SCAN
rs35352346	PPP2R3A	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135862000-135904800	Weak transcription	Hela-S3	cervix
2	chr3:135864200-135882400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:135864400-135882600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:135864400-135885200	Weak transcription	Brain Germinal Matrix	brain
5	chr3:135865600-135882400	Weak transcription	Fetal Heart	heart
6	chr3:135868800-135883000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:135869800-135882400	Weak transcription	Brain Angular Gyrus	brain
8	chr3:135870800-135895200	Weak transcription	Fetal Intestine Small	intestine
9	chr3:135871000-135881800	Weak transcription	Right Ventricle	heart
10	chr3:135871000-135882400	Weak transcription	Esophagus	oesophagus
11	chr3:135871000-135882400	Weak transcription	Small Intestine	intestine
12	chr3:135871000-135897600	Weak transcription	Aorta	Aorta
13	chr3:135871200-135882200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:135871200-135905000	Weak transcription	Fetal Stomach	stomach
15	chr3:135871400-135882200	Weak transcription	HUVEC	blood vessel
16	chr3:135871400-135882400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:135871400-135885000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:135871400-135885000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:135871400-135885600	Weak transcription	Fetal Kidney	kidney
20	chr3:135871600-135881800	Weak transcription	Brain Substantia Nigra	brain
21	chr3:135871600-135882200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:135871600-135882400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:135871600-135882400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:135871600-135882400	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:135871600-135883000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:135871600-135884800	Weak transcription	K562	blood
27	chr3:135871600-135885000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:135871800-135882200	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr3:135872000-135882200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:135872000-135882200	Weak transcription	Primary B cells from cord blood	blood
31	chr3:135872000-135882200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr3:135872000-135882400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:135872000-135882400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:135872000-135882400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:135872000-135882400	Weak transcription	Fetal Lung	lung
36	chr3:135872000-135885000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:135872000-135887800	Weak transcription	HSMM	muscle
38	chr3:135872200-135882200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:135872200-135891400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:135872600-135882200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:135872600-135882200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:135872800-135885400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:135872800-135903600	Weak transcription	Thymus	Thymus
44	chr3:135873600-135881800	Weak transcription	Liver	Liver
45	chr3:135873600-135882400	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:135873600-135889800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:135874400-135887400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr3:135874600-135882200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr3:135874800-135882400	Weak transcription	Pancreas	Pancrea
50	chr3:135874800-135882400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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