Variant report

Variant	rs10460508
Chromosome Location	chr2:55882565-55882566
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10165864	0.82[CEU][hapmap]
rs10496050	0.82[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs1084522	0.96[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs1084525	0.85[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs12329050	0.90[YRI][hapmap]
rs17278044	0.96[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs17369191	0.96[CEU][hapmap];0.90[YRI][hapmap]
rs1823893	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs1975484	0.96[CEU][hapmap]
rs1975487	0.92[CEU][hapmap];0.85[YRI][hapmap]
rs2586947	0.81[AFR][1000 genomes]
rs2586950	0.81[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2586952	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2586954	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2586969	0.81[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs2586970	0.81[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs2627759	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2627765	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2627766	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2627767	0.90[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs2627769	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2627772	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2627773	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2627775	0.94[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2627776	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2627777	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2627779	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35504023	0.82[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs4290693	0.82[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs4312532	0.82[CEU][hapmap];0.95[YRI][hapmap]
rs4672052	0.91[CEU][hapmap]
rs62165255	0.80[AMR][1000 genomes]
rs6545506	0.82[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs706548	0.85[CEU][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap]
rs7582278	0.92[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs7589673	0.81[EUR][1000 genomes]
rs7596377	0.91[YRI][hapmap]
rs782566	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782567	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs782568	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782572	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782573	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs782579	0.84[ASN][1000 genomes]
rs782584	0.89[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs782585	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs782586	0.82[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs782588	0.96[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs782590	0.92[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs782594	0.80[EUR][1000 genomes]
rs782595	0.96[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs782599	0.82[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs782600	0.81[AFR][1000 genomes]
rs782601	0.81[AFR][1000 genomes]
rs782602	0.82[ASW][hapmap];0.85[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs782606	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs782619	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782622	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs782629	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782630	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782632	0.85[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782633	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782634	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs782637	0.94[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782641	0.82[AMR][1000 genomes]
rs782642	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs782644	0.80[AMR][1000 genomes]
rs782649	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs782650	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs782652	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs809732	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs935177	0.81[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs9917139	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv9791	chr2:55872725-55883751	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10460508	PNPT1	cis	lymphoblastoid	seeQTL
rs10460508	SMEK2	cis	parietal	SCAN
rs10460508	CCDC104	cis	parietal	SCAN
rs10460508	PNPT1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
4	chr2:55849800-55882800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
6	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
7	chr2:55864000-55893200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:55864200-55882800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:55864400-55919600	Weak transcription	NHLF	lung
10	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:55870400-55887600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:55870400-55887800	Weak transcription	Fetal Brain Female	brain
13	chr2:55870400-55920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:55870600-55892800	Weak transcription	Psoas Muscle	Psoas
15	chr2:55870600-55920000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:55870800-55888000	Weak transcription	Colonic Mucosa	Colon
17	chr2:55870800-55893400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:55870800-55903600	Weak transcription	Gastric	stomach
19	chr2:55870800-55909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:55870800-55920400	Weak transcription	Aorta	Aorta
21	chr2:55871000-55887800	Weak transcription	Esophagus	oesophagus
22	chr2:55871000-55893200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:55871000-55893200	Weak transcription	Thymus	Thymus
24	chr2:55871000-55920000	Weak transcription	Spleen	Spleen
25	chr2:55871200-55893400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:55871200-55905200	Weak transcription	Brain Angular Gyrus	brain
27	chr2:55871400-55882600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:55871400-55905200	Weak transcription	Fetal Kidney	kidney
29	chr2:55873000-55888400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr2:55873200-55893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:55873200-55919800	Weak transcription	Small Intestine	intestine
32	chr2:55873800-55882600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:55873800-55899400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:55874800-55920200	Weak transcription	Pancreas	Pancrea
35	chr2:55875600-55887200	Weak transcription	K562	blood
36	chr2:55878800-55884400	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:55879000-55882800	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:55879000-55883000	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr2:55879000-55883000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:55879000-55883200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr2:55879000-55883200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:55879000-55883400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:55879000-55883400	Strong transcription	Primary T cells from cord blood	blood
44	chr2:55879000-55883400	Strong transcription	A549	lung
45	chr2:55879000-55883600	Strong transcription	Dnd41	blood
46	chr2:55879000-55883800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr2:55879000-55883800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:55879000-55888800	Strong transcription	Liver	Liver
49	chr2:55879000-55889000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:55879000-55890400	Strong transcription	Fetal Muscle Leg	muscle

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