Variant report

Variant	rs10175828
Chromosome Location	chr2:234381817-234381818
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234368802..234371740-chr2:234380703..234384400,4	MCF-7	breast:
2	chr2:234365726..234368182-chr2:234381553..234383483,3	MCF-7	breast:
3	chr2:234379094..234382048-chr2:234385373..234387118,2	K562	blood:
4	chr2:234377919..234380691-chr2:234381184..234384244,3	MCF-7	breast:
5	chr2:234378675..234382523-chr2:234390792..234394362,4	K562	blood:
6	chr2:234381434..234384275-chr2:234387365..234389292,3	K562	blood:

Variant related genes	Relation type
ENSG00000077044	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13016839	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.88[ASN][1000 genomes]
rs13028688	0.81[ASN][1000 genomes]
rs2276566	0.89[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34013402	0.87[EUR][1000 genomes]
rs60064064	0.88[ASN][1000 genomes]
rs71421698	0.81[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	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv1000870	chr2:234333083-234410768	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10175828	USP40	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234339600-234394200	Weak transcription	HUVEC	blood vessel
2	chr2:234339800-234391400	Weak transcription	NHDF-Ad	bronchial
3	chr2:234343000-234393000	Strong transcription	Primary T cells from cord blood	blood
4	chr2:234343000-234402200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:234343200-234383000	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:234344000-234382000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:234344200-234382000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:234344200-234382200	Strong transcription	Primary B cells from cord blood	blood
9	chr2:234344200-234382600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr2:234352400-234382000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:234352600-234382600	Strong transcription	Primary B cells from peripheral blood	blood
12	chr2:234352600-234382600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:234352800-234382000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:234357600-234382000	Strong transcription	Liver	Liver
15	chr2:234361200-234389800	Weak transcription	Fetal Kidney	kidney
16	chr2:234362400-234384600	Strong transcription	Spleen	Spleen
17	chr2:234363800-234390600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:234364000-234411200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:234365800-234393600	Weak transcription	Hela-S3	cervix
20	chr2:234370000-234382000	Strong transcription	Thymus	Thymus
21	chr2:234373000-234392200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:234373000-234409800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:234373200-234382800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:234373400-234391000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:234373800-234384200	Weak transcription	Osteobl	bone
26	chr2:234373800-234404400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr2:234375200-234388000	Strong transcription	Lung	lung
28	chr2:234375400-234411200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:234375600-234387400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:234376000-234389400	Weak transcription	NH-A	brain
31	chr2:234376200-234382800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:234376200-234390200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr2:234377800-234385600	Weak transcription	Aorta	Aorta
34	chr2:234377800-234391400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:234377800-234397200	Weak transcription	Small Intestine	intestine
36	chr2:234378000-234384000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:234378000-234387000	Weak transcription	HSMM	muscle
38	chr2:234378200-234395000	Weak transcription	Right Atrium	heart
39	chr2:234378400-234388000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:234378400-234390200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:234378400-234390800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr2:234378400-234391000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr2:234378600-234383000	Weak transcription	K562	blood
44	chr2:234378600-234383000	Weak transcription	NHLF	lung
45	chr2:234378600-234391600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:234378800-234384200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:234378800-234384800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr2:234378800-234391400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:234379000-234383400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:234379000-234386600	Weak transcription	HepG2	liver

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