Variant report

Variant	rs782652
Chromosome Location	chr2:55862775-55862776
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55857547..55860047-chr2:55862706..55864207,2	MCF-7	breast:
2	chr2:55862409..55864848-chr2:55873720..55876031,2	K562	blood:

Variant related genes	Relation type
ENSG00000138035	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10165864	0.82[CEU][hapmap]
rs10460508	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]
rs10496050	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1058582	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1084522	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1084525	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap]
rs11125581	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12329050	0.85[YRI][hapmap]
rs17278044	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17369191	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17798852	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1823893	0.96[CEU][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1975484	0.96[CEU][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1975487	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs2586947	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2586950	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2586952	0.86[AFR][1000 genomes]
rs2586954	0.82[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2586968	0.85[AFR][1000 genomes]
rs2586969	0.81[CEU][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs2586970	0.81[CEU][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs2627759	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2627765	0.82[ASW][hapmap];0.85[CEU][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs2627766	0.84[AFR][1000 genomes]
rs2627772	0.86[AFR][1000 genomes]
rs2627773	0.85[CEU][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2627775	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2627776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2627777	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2627779	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2627780	0.83[AFR][1000 genomes]
rs2627782	0.85[AFR][1000 genomes]
rs35504023	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3762513	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4290693	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4312532	0.82[CEU][hapmap];0.90[YRI][hapmap]
rs4672052	0.91[CEU][hapmap]
rs4672054	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4672055	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4672056	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55761024	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58003472	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62165173	0.82[AMR][1000 genomes]
rs62165181	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62165182	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62165183	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62165184	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62165196	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62165197	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62165200	0.80[AFR][1000 genomes]
rs6545506	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs706548	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7582278	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes]
rs7594279	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7596377	0.86[YRI][hapmap]
rs7598650	0.83[AMR][1000 genomes]
rs782566	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs782567	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs782568	0.82[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs782572	0.89[CEU][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap]
rs782573	0.89[CEU][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap]
rs782584	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap]
rs782586	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782587	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782588	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782590	0.94[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782594	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782595	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782599	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782600	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782601	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782602	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782606	0.82[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs782629	0.88[ASW][hapmap];0.85[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs782630	0.87[CEU][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs782632	0.85[CEU][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs782633	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs782634	0.83[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs782637	0.88[ASW][hapmap];0.82[CEU][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs782649	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs782650	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs809732	0.89[CEU][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap]
rs935177	0.81[CEU][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs9917139	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs782652	SMEK2	cis	parietal	SCAN
rs782652	PNPT1	Cis_1M	lymphoblastoid	RTeQTL
rs782652	PNPT1	cis	cerebellum	SCAN
rs782652	CCDC104	cis	parietal	SCAN
rs782652	PNPT1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846400-55870000	Weak transcription	Aorta	Aorta
2	chr2:55846600-55862800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:55846600-55863400	Weak transcription	Fetal Kidney	kidney
4	chr2:55846600-55870000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:55846600-55870000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:55846800-55863400	Weak transcription	HSMMtube	muscle
7	chr2:55846800-55863400	Weak transcription	NHLF	lung
8	chr2:55846800-55863800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:55847600-55864200	Weak transcription	Brain Germinal Matrix	brain
12	chr2:55847600-55870000	Weak transcription	Colonic Mucosa	Colon
13	chr2:55847600-55870000	Weak transcription	Psoas Muscle	Psoas
14	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
15	chr2:55847800-55863400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:55848000-55862800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:55848000-55872600	Weak transcription	Small Intestine	intestine
18	chr2:55849200-55862800	Weak transcription	Left Ventricle	heart
19	chr2:55849200-55863600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:55849200-55865200	Weak transcription	Gastric	stomach
21	chr2:55849200-55865600	Weak transcription	Fetal Brain Female	brain
22	chr2:55849200-55867400	Weak transcription	Lung	lung
23	chr2:55849200-55868200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:55849200-55868200	Weak transcription	Right Ventricle	heart
25	chr2:55849200-55869400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:55849200-55873200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:55849400-55862800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:55849400-55862800	Weak transcription	Placenta	Placenta
29	chr2:55849400-55863400	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:55849400-55867400	Weak transcription	Thymus	Thymus
31	chr2:55849600-55862800	Weak transcription	Fetal Lung	lung
32	chr2:55849800-55863400	Weak transcription	HepG2	liver
33	chr2:55849800-55863800	Weak transcription	Esophagus	oesophagus
34	chr2:55849800-55869400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr2:55849800-55882800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:55851200-55862800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:55851200-55863800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:55851400-55870000	Weak transcription	Spleen	Spleen
39	chr2:55852000-55865800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr2:55852000-55872400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:55853000-55863400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:55853200-55862800	Weak transcription	NHEK	skin
43	chr2:55853200-55864000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr2:55853400-55863800	Weak transcription	Brain Anterior Caudate	brain
45	chr2:55853600-55863400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr2:55853600-55882400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr2:55856400-55863600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr2:55857000-55873800	Strong transcription	Fetal Thymus	thymus
49	chr2:55857600-55869800	Weak transcription	Brain Angular Gyrus	brain
50	chr2:55857800-55863200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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