Variant report

Variant	rs910819
Chromosome Location	chr10:52222605-52222606
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52220837..52222946-chr10:52225601..52227528,3	K562	blood:
2	chr10:52221096..52222915-chr10:52233294..52234795,2	K562	blood:
3	chr10:52220084..52221898-chr10:52222216..52224809,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction

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

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

rs_ID	r²[population]
rs1203374	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203379	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203380	0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs1203383	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[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];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203384	1.00[CEU][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]
rs1203391	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]
rs1203402	0.90[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203412	1.00[CEU][hapmap];0.90[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];0.90[EUR][1000 genomes]
rs1203427	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209146	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1211373	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1212555	0.89[TSI][hapmap]
rs1810576	0.83[AFR][1000 genomes]
rs2024871	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064760	0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs2208035	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.95[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	0.89[EUR][1000 genomes]
rs2983348	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983349	0.89[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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011711	0.85[TSI][hapmap]
rs3011712	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011715	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011768	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011795	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[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	0.89[EUR][1000 genomes]
rs9416590	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[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
rs910819	PTPRN2	trans	lymphoblastoid	seeQTL
rs910819	CSTF2T	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52192400-52229400	Weak transcription	Aorta	Aorta
2	chr10:52192400-52230400	Weak transcription	HSMM	muscle
3	chr10:52197800-52229800	Weak transcription	Gastric	stomach
4	chr10:52204400-52228600	Weak transcription	NHDF-Ad	bronchial
5	chr10:52208000-52240200	Weak transcription	Esophagus	oesophagus
6	chr10:52208200-52229600	Weak transcription	Right Ventricle	heart
7	chr10:52208400-52230400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:52209600-52229200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr10:52211600-52223800	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:52211800-52229400	Weak transcription	NHEK	skin
11	chr10:52212800-52229400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr10:52212800-52229600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr10:52215000-52230400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr10:52215200-52228800	Weak transcription	HepG2	liver
15	chr10:52215200-52229000	Weak transcription	Brain Angular Gyrus	brain
16	chr10:52215600-52228600	Weak transcription	HSMMtube	muscle
17	chr10:52215800-52228600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr10:52216400-52228600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr10:52217200-52229600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr10:52218000-52240200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr10:52218200-52228800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr10:52218200-52230800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr10:52218400-52229400	Weak transcription	A549	lung
24	chr10:52218600-52228400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr10:52219000-52223400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr10:52219000-52223600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr10:52219400-52226000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr10:52219800-52229000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr10:52220000-52243600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr10:52220200-52230400	Weak transcription	Hela-S3	cervix
31	chr10:52220400-52223600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr10:52220400-52224000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr10:52220400-52224000	Weak transcription	Fetal Heart	heart
34	chr10:52220400-52226800	Weak transcription	Fetal Brain Male	brain
35	chr10:52220400-52227600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr10:52220400-52227800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr10:52220400-52228400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr10:52220400-52228400	Weak transcription	Fetal Kidney	kidney
39	chr10:52220400-52228800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr10:52220400-52228800	Weak transcription	Primary B cells from cord blood	blood
41	chr10:52220400-52229000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr10:52220400-52229000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr10:52220400-52229000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr10:52220400-52229000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr10:52220400-52229000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr10:52220400-52229000	Weak transcription	Placenta	Placenta
47	chr10:52220400-52229200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr10:52220400-52229200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr10:52220400-52229200	Weak transcription	Fetal Lung	lung
50	chr10:52220400-52229600	Weak transcription	Fetal Thymus	thymus

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