Variant report

Variant	rs1975487
Chromosome Location	chr2:55809054-55809055
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	chr2:55807623..55810451-chr2:55815927..55817917,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10165864	0.81[CEU][hapmap]
rs10454749	0.82[AMR][1000 genomes]
rs10460508	0.92[CEU][hapmap];0.85[YRI][hapmap]
rs10496050	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1058582	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1084522	0.96[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1084525	0.81[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs11125581	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17278044	0.96[CEU][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17369191	0.96[CEU][hapmap];0.82[JPT][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17798852	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1823893	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1975484	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2054728	0.91[AFR][1000 genomes]
rs2586947	0.83[EUR][1000 genomes]
rs2586950	0.91[JPT][hapmap];0.86[YRI][hapmap]
rs2586954	0.92[CEU][hapmap];0.85[YRI][hapmap]
rs2586969	0.92[CEU][hapmap];0.86[YRI][hapmap]
rs2586970	0.92[CEU][hapmap];0.86[YRI][hapmap]
rs2627759	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2627765	0.80[CEU][hapmap];0.85[YRI][hapmap]
rs2627767	0.91[YRI][hapmap]
rs2627773	0.85[CEU][hapmap];0.86[YRI][hapmap]
rs2627775	0.81[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs2627776	0.92[CEU][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap]
rs35504023	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3762513	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4290693	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4312532	0.82[YRI][hapmap];0.93[AFR][1000 genomes]
rs4672052	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4672054	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4672055	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4672056	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55761024	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58003472	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62165173	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62165181	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62165182	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62165183	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62165184	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62165196	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62165197	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545506	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6739513	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs706548	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs7582278	0.85[CEU][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7594279	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7598650	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs782568	0.92[CEU][hapmap];0.85[YRI][hapmap]
rs782572	0.85[CEU][hapmap]
rs782573	0.85[CEU][hapmap]
rs782584	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs782586	0.96[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs782587	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs782588	0.96[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs782590	0.92[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs782594	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs782595	0.96[CEU][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs782599	0.82[CEU][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs782600	0.83[EUR][1000 genomes]
rs782601	0.83[EUR][1000 genomes]
rs782602	0.85[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs782606	0.92[CEU][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap]
rs782613	0.92[AFR][1000 genomes]
rs782629	0.84[CEU][hapmap];0.85[YRI][hapmap]
rs782630	0.87[CEU][hapmap];0.89[YRI][hapmap]
rs782632	0.85[CEU][hapmap];0.86[YRI][hapmap]
rs782634	0.86[YRI][hapmap]
rs782637	0.81[CEU][hapmap];0.85[YRI][hapmap]
rs782649	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs782650	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs782652	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs809732	0.85[CEU][hapmap]
rs935177	0.92[CEU][hapmap];0.86[YRI][hapmap]
rs9917139	0.81[CEU][hapmap]

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	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1975487	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	chr2:55769600-55816000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:55770400-55818200	Weak transcription	Small Intestine	intestine
4	chr2:55770600-55821600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr2:55770800-55815800	Strong transcription	Liver	Liver
6	chr2:55779600-55816200	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:55779600-55831400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:55788600-55816600	Strong transcription	Primary B cells from peripheral blood	blood
9	chr2:55788800-55825200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:55789800-55822800	Weak transcription	HSMMtube	muscle
11	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:55790200-55812800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:55790200-55829000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
15	chr2:55790400-55836200	Weak transcription	Fetal Heart	heart
16	chr2:55790800-55816600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:55790800-55819400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:55791200-55812200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:55793400-55817000	Strong transcription	Fetal Thymus	thymus
20	chr2:55794200-55818200	Weak transcription	Psoas Muscle	Psoas
21	chr2:55794400-55812200	Weak transcription	NHLF	lung
22	chr2:55794400-55825200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:55794400-55829000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:55794800-55816200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr2:55796800-55823800	Weak transcription	Thymus	Thymus
26	chr2:55796800-55825200	Weak transcription	Brain Substantia Nigra	brain
27	chr2:55796800-55825600	Weak transcription	Pancreas	Pancrea
28	chr2:55796800-55829400	Weak transcription	Esophagus	oesophagus
29	chr2:55796800-55842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:55797000-55811400	Weak transcription	Brain Germinal Matrix	brain
31	chr2:55797000-55818200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:55797000-55824200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:55797000-55828000	Weak transcription	Aorta	Aorta
34	chr2:55797000-55829400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:55797000-55829600	Weak transcription	Gastric	stomach
36	chr2:55797600-55810600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:55798000-55812200	Weak transcription	Brain Angular Gyrus	brain
38	chr2:55799600-55810600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr2:55800400-55809200	Strong transcription	Dnd41	blood
40	chr2:55800800-55812200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:55801400-55820000	Weak transcription	Ovary	ovary
42	chr2:55802200-55812600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr2:55802200-55815800	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr2:55802200-55818200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:55802400-55809400	Strong transcription	A549	lung
46	chr2:55802400-55810000	Strong transcription	GM12878-XiMat	blood
47	chr2:55802400-55816200	Strong transcription	Placenta	Placenta
48	chr2:55802400-55816800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:55802400-55816800	Strong transcription	HepG2	liver
50	chr2:55802600-55809200	Strong transcription	HUES64 Cell Line	embryonic stem cell

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