Variant report

Variant	rs1203391
Chromosome Location	chr10:52205146-52205147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52199893..52201805-chr10:52203419..52206353,2	K562	blood:
2	chr10:52199832..52201783-chr10:52205010..52207996,2	K562	blood:
3	chr10:52205018..52207275-chr10:52208776..52210388,2	K562	blood:
4	chr10:52201084..52203471-chr10:52204714..52206588,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1203374	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203379	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203380	0.83[TSI][hapmap]
rs1203383	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203384	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203402	0.90[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203412	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203416	1.00[ASN][1000 genomes]
rs1203417	1.00[ASN][1000 genomes]
rs1203419	1.00[ASN][1000 genomes]
rs1203422	1.00[ASN][1000 genomes]
rs1203426	0.82[CEU][hapmap];0.98[EUR][1000 genomes]
rs1203427	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209146	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1211373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1212555	0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs1810576	0.80[AFR][1000 genomes]
rs2024871	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064760	0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs2208035	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474611	1.00[ASN][1000 genomes]
rs2574945	1.00[ASN][1000 genomes]
rs2574976	0.93[GIH][hapmap];1.00[ASN][1000 genomes]
rs2688874	1.00[ASN][1000 genomes]
rs2688876	1.00[ASN][1000 genomes]
rs2688883	1.00[ASN][1000 genomes]
rs2688884	0.93[GIH][hapmap];1.00[ASN][1000 genomes]
rs2842099	1.00[ASN][1000 genomes]
rs2842110	1.00[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs2860490	0.85[TSI][hapmap]
rs2983346	0.80[EUR][1000 genomes]
rs2983348	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983349	0.80[EUR][1000 genomes]
rs2983352	0.82[TSI][hapmap]
rs2983362	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs2983363	0.85[TSI][hapmap]
rs2983372	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011711	0.85[TSI][hapmap]
rs3011712	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011715	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011768	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011795	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078586	0.86[TSI][hapmap]
rs7094723	0.80[CEU][hapmap]
rs72801753	1.00[ASN][1000 genomes]
rs7923756	1.00[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs910818	0.80[EUR][1000 genomes]
rs910819	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9416590	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1203391	CSTF2T	cis	parietal	SCAN
rs1203391	PTPRN2	trans	lymphoblastoid	seeQTL

Chromatin state (count:42 , 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	chr10:52179000-52205800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr10:52179000-52207600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr10:52179000-52209000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr10:52181600-52219400	Weak transcription	Placenta	Placenta
8	chr10:52181800-52206200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr10:52182200-52220000	Weak transcription	Fetal Stomach	stomach
10	chr10:52191600-52207600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr10:52191600-52211200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr10:52191800-52205400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr10:52191800-52219600	Weak transcription	Fetal Lung	lung
14	chr10:52192000-52219600	Weak transcription	Adipose Nuclei	Adipose
15	chr10:52192400-52207600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr10:52192400-52219400	Weak transcription	Liver	Liver
17	chr10:52192400-52219600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr10:52192400-52219600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr10:52192400-52220000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr10:52192400-52229400	Weak transcription	Aorta	Aorta
21	chr10:52192400-52230400	Weak transcription	HSMM	muscle
22	chr10:52193000-52207400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr10:52193400-52205400	Weak transcription	Primary B cells from cord blood	blood
24	chr10:52193400-52206200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr10:52194200-52207600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr10:52197600-52207600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr10:52197800-52229800	Weak transcription	Gastric	stomach
28	chr10:52198200-52207600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr10:52198400-52207400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr10:52199200-52207400	Weak transcription	Brain Anterior Caudate	brain
31	chr10:52200200-52207600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr10:52200800-52206000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr10:52200800-52216000	Weak transcription	K562	blood
34	chr10:52201000-52214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr10:52201400-52206200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr10:52202200-52214000	Weak transcription	Fetal Heart	heart
37	chr10:52203000-52206200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr10:52203000-52219400	Weak transcription	Ovary	ovary
39	chr10:52203200-52219400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr10:52203800-52219400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr10:52204400-52228600	Weak transcription	NHDF-Ad	bronchial
42	chr10:52204600-52206200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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