Variant report

Variant	rs2627775
Chromosome Location	chr2:55877113-55877114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55876589..55879257-chr2:55911121..55913801,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10460508	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]
rs10496050	0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs1084522	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs1084525	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap]
rs12329050	0.90[YRI][hapmap]
rs17278044	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17369191	0.85[CEU][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap]
rs1823893	0.85[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs1975484	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs1975487	0.81[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs2586947	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2586950	1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2586952	0.83[AFR][1000 genomes]
rs2586954	0.94[ASW][hapmap];0.89[CEU][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2586969	1.00[YRI][hapmap]
rs2586970	1.00[YRI][hapmap]
rs2627759	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2627765	0.94[ASW][hapmap];0.88[LWK][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2627766	0.83[AFR][1000 genomes]
rs2627773	0.83[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2627776	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2627777	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2627779	0.81[AFR][1000 genomes]
rs35504023	0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4290693	0.85[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs4312532	0.95[YRI][hapmap]
rs4672056	0.80[AFR][1000 genomes]
rs58003472	0.80[AFR][1000 genomes]
rs6545506	0.85[CEU][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs706548	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7582278	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7596377	0.91[YRI][hapmap]
rs782566	0.86[AFR][1000 genomes]
rs782567	0.87[AFR][1000 genomes]
rs782568	0.94[ASW][hapmap];0.89[CEU][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs782572	0.83[JPT][hapmap];0.86[YRI][hapmap]
rs782573	0.83[JPT][hapmap];0.86[YRI][hapmap]
rs782584	0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.86[YRI][hapmap]
rs782586	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs782587	0.86[ASN][1000 genomes]
rs782588	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs782590	0.81[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs782594	0.86[ASN][1000 genomes]
rs782595	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs782599	0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs782600	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs782601	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs782602	0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs782606	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs782629	0.88[ASW][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs782630	0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs782632	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs782633	0.81[AFR][1000 genomes]
rs782634	0.83[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs782637	0.88[ASW][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs782649	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs782650	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs782652	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]
rs809732	0.83[JPT][hapmap];0.86[YRI][hapmap]
rs935177	1.00[YRI][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2627775	PNPT1	cis	lymphoblastoid	seeQTL
rs2627775	PNPT1	cis	cerebellum	SCAN
rs2627775	PNPT1	Cis_1M	lymphoblastoid	RTeQTL
rs2627775	RPS27A	cis	frontal cortex	BrainEAC
rs2627775	SMEK2	cis	parietal	SCAN
rs2627775	CCDC104	cis	cerebellum	SCAN
rs2627775	CCDC104	cis	parietal	SCAN

Chromatin state (count:123 , 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	chr2:55853600-55882400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
7	chr2:55858800-55877200	Strong transcription	Dnd41	blood
8	chr2:55859000-55877200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:55859400-55877600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
11	chr2:55862000-55877200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:55862000-55877800	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:55864000-55893200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:55864200-55882800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:55864400-55919600	Weak transcription	NHLF	lung
16	chr2:55864600-55881400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr2:55864600-55881400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr2:55864800-55879200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:55865000-55880400	Weak transcription	HMEC	breast
20	chr2:55866200-55882400	Weak transcription	Ovary	ovary
21	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr2:55868000-55879200	Weak transcription	NH-A	brain
23	chr2:55870400-55887600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:55870400-55887800	Weak transcription	Fetal Brain Female	brain
25	chr2:55870400-55920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:55870600-55879800	Weak transcription	HUVEC	blood vessel
27	chr2:55870600-55881400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:55870600-55892800	Weak transcription	Psoas Muscle	Psoas
29	chr2:55870600-55920000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:55870800-55879200	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:55870800-55888000	Weak transcription	Colonic Mucosa	Colon
32	chr2:55870800-55893400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:55870800-55903600	Weak transcription	Gastric	stomach
34	chr2:55870800-55909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:55870800-55920400	Weak transcription	Aorta	Aorta
36	chr2:55871000-55879000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:55871000-55880000	Weak transcription	Right Ventricle	heart
38	chr2:55871000-55880600	Weak transcription	Lung	lung
39	chr2:55871000-55887800	Weak transcription	Esophagus	oesophagus
40	chr2:55871000-55893200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:55871000-55893200	Weak transcription	Thymus	Thymus
42	chr2:55871000-55920000	Weak transcription	Spleen	Spleen
43	chr2:55871200-55879000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:55871200-55879200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:55871200-55880000	Weak transcription	Brain Substantia Nigra	brain
46	chr2:55871200-55880400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:55871200-55880600	Weak transcription	Colon Smooth Muscle	Colon
48	chr2:55871200-55893400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr2:55871200-55905200	Weak transcription	Brain Angular Gyrus	brain
50	chr2:55871400-55882600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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