Variant report

Variant	rs2586965
Chromosome Location	chr2:55823305-55823306
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55816894..55821327-chr2:55821705..55825491,6	K562	blood:
2	chr2:55818907..55824295-chr2:55841098..55846037,6	MCF-7	breast:
3	chr2:55820891..55824510-chr2:55834569..55837738,3	K562	blood:

Variant related genes	Relation type
ENSG00000138041	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1037508	0.83[ASN][1000 genomes]
rs10427222	0.81[JPT][hapmap]
rs1045910	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12463766	0.82[ASN][1000 genomes]
rs12617829	0.89[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs12619756	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713301	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12989898	0.81[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs13016772	0.84[ASN][1000 genomes]
rs13028892	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs13427693	0.93[EUR][1000 genomes]
rs13430657	0.93[EUR][1000 genomes]
rs1373228	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1563201	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs17792467	1.00[YRI][hapmap]
rs1814457	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1975485	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1975486	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2168097	0.93[ASN][1000 genomes]
rs2586946	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2586948	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2586949	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2586951	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2586955	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2586958	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2586959	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2586960	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2586961	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2627758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627768	0.80[AMR][1000 genomes]
rs2627771	0.81[ASN][1000 genomes]
rs2627774	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2627778	0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2627781	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2627783	0.88[ASN][1000 genomes]
rs3748945	0.80[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs3816489	0.80[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4233962	0.83[ASN][1000 genomes]
rs4671248	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs61475257	0.88[ASN][1000 genomes]
rs62165178	0.84[ASN][1000 genomes]
rs6545503	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6545505	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6731927	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs706549	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs706550	0.90[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs706551	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs730884	0.88[ASN][1000 genomes]
rs744514	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7559307	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7585484	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7605486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7605504	0.93[ASN][1000 genomes]
rs782569	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs782570	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782571	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs782574	0.89[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782575	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782576	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs782577	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782580	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782582	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782583	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782589	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs782591	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs782593	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs782597	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs782598	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs782603	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs782604	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs782612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782614	0.87[ASN][1000 genomes]
rs782615	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782617	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782618	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782620	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782621	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782623	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782624	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782625	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs782626	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782627	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs782628	0.89[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs782631	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs782635	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs782636	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs782638	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs782643	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs782647	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs782648	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs782651	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9636439	0.80[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2586965	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
2	chr2:55779600-55831400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:55788800-55825200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:55790200-55829000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
7	chr2:55790400-55836200	Weak transcription	Fetal Heart	heart
8	chr2:55794400-55825200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:55794400-55829000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:55796800-55823800	Weak transcription	Thymus	Thymus
11	chr2:55796800-55825200	Weak transcription	Brain Substantia Nigra	brain
12	chr2:55796800-55825600	Weak transcription	Pancreas	Pancrea
13	chr2:55796800-55829400	Weak transcription	Esophagus	oesophagus
14	chr2:55796800-55842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:55797000-55824200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:55797000-55828000	Weak transcription	Aorta	Aorta
17	chr2:55797000-55829400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:55797000-55829600	Weak transcription	Gastric	stomach
19	chr2:55803000-55838800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:55803200-55823800	Weak transcription	Lung	lung
21	chr2:55804000-55824000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:55804400-55825200	Weak transcription	K562	blood
23	chr2:55806600-55825600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:55806800-55825200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:55808200-55824800	Weak transcription	Colonic Mucosa	Colon
26	chr2:55810600-55829600	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:55811400-55829400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:55811600-55825000	Weak transcription	Fetal Brain Female	brain
29	chr2:55812400-55823400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr2:55814200-55825200	Weak transcription	HUVEC	blood vessel
31	chr2:55814200-55825600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:55814200-55829000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:55814200-55829400	Weak transcription	Brain Germinal Matrix	brain
34	chr2:55814400-55824200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:55814400-55826000	Weak transcription	GM12878-XiMat	blood
36	chr2:55815200-55825400	Weak transcription	Hela-S3	cervix
37	chr2:55815400-55823800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:55816000-55823400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:55816000-55824800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:55816200-55825000	Weak transcription	Placenta	Placenta
41	chr2:55816400-55825200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:55816800-55823400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:55818000-55827400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:55818400-55825000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:55818400-55825000	Weak transcription	A549	lung
46	chr2:55818400-55825000	Weak transcription	Osteobl	bone
47	chr2:55818400-55825400	Weak transcription	NH-A	brain
48	chr2:55818400-55825600	Weak transcription	NHDF-Ad	bronchial
49	chr2:55818400-55825800	Weak transcription	NHLF	lung
50	chr2:55818600-55823400	Weak transcription	Muscle Satellite Cultured Cells	--

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