Variant report

Variant	rs1203387
Chromosome Location	chr10:52206378-52206379
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52199832..52201783-chr10:52205010..52207996,2	K562	blood:
2	chr10:52205018..52207275-chr10:52208776..52210388,2	K562	blood:
3	chr10:52201084..52203471-chr10:52204714..52206588,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1203381	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203388	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203389	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203392	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203396	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203400	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203404	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1210065	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1210066	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211496	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1740759	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2461912	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7099450	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs7893281	0.99[ASN][1000 genomes]
rs927046	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1203387	MSMB	cis	parietal	SCAN
rs1203387	CSTF2T	cis	parietal	SCAN
rs1203387	PARG	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52178400-52220000	Weak transcription	Pancreas	Pancrea
2	chr10:52178600-52217200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:52178600-52219400	Weak transcription	Left Ventricle	heart
4	chr10:52179000-52207600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr10:52179000-52209000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr10:52181600-52219400	Weak transcription	Placenta	Placenta
7	chr10:52182200-52220000	Weak transcription	Fetal Stomach	stomach
8	chr10:52191600-52207600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr10:52191600-52211200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr10:52191800-52219600	Weak transcription	Fetal Lung	lung
11	chr10:52192000-52219600	Weak transcription	Adipose Nuclei	Adipose
12	chr10:52192400-52207600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr10:52192400-52219400	Weak transcription	Liver	Liver
14	chr10:52192400-52219600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr10:52192400-52219600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr10:52192400-52220000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr10:52192400-52229400	Weak transcription	Aorta	Aorta
18	chr10:52192400-52230400	Weak transcription	HSMM	muscle
19	chr10:52193000-52207400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr10:52194200-52207600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr10:52197600-52207600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr10:52197800-52229800	Weak transcription	Gastric	stomach
23	chr10:52198200-52207600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr10:52198400-52207400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr10:52199200-52207400	Weak transcription	Brain Anterior Caudate	brain
26	chr10:52200200-52207600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr10:52200800-52216000	Weak transcription	K562	blood
28	chr10:52201000-52214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr10:52202200-52214000	Weak transcription	Fetal Heart	heart
30	chr10:52203000-52219400	Weak transcription	Ovary	ovary
31	chr10:52203200-52219400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr10:52203800-52219400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr10:52204400-52228600	Weak transcription	NHDF-Ad	bronchial
34	chr10:52205400-52206600	ZNF genes & repeats	Primary B cells from cord blood	blood
35	chr10:52205600-52206600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr10:52206200-52206400	ZNF genes & repeats	Primary T cells from cord blood	blood
37	chr10:52206200-52206600	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr10:52206200-52206600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
39	chr10:52206200-52206600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
40	chr10:52206200-52206600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
41	chr10:52206200-52206800	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr10:52206200-52206800	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr10:52206200-52207000	Enhancers	HUES48 Cell Line	embryonic stem cell

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