Variant report

Variant	rs6545505
Chromosome Location	chr2:55758653-55758654
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	chr2:55746672..55749333-chr2:55758426..55761891,4	K562	blood:
2	chr2:55745428..55748041-chr2:55756685..55759151,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163001	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10184287	0.89[CEU][hapmap]
rs1037508	0.85[ASN][1000 genomes]
rs10427222	0.81[JPT][hapmap]
rs1045910	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12463766	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12617829	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs12619756	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12989898	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs13016772	0.86[ASN][1000 genomes]
rs13028892	1.00[CEU][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1373228	0.96[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs1563201	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1814457	0.88[ASN][1000 genomes]
rs1975486	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs2168097	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2586946	0.94[ASN][1000 genomes]
rs2586948	0.94[ASN][1000 genomes]
rs2586949	0.83[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2586951	0.82[ASN][1000 genomes]
rs2586965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2627758	0.95[ASN][1000 genomes]
rs2627763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2627778	0.96[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs2627783	0.83[ASN][1000 genomes]
rs3748945	0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs3816489	0.83[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4233962	0.85[ASN][1000 genomes]
rs4671248	1.00[CEU][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61475257	0.91[ASN][1000 genomes]
rs62165178	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545503	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6716100	0.83[JPT][hapmap]
rs6731927	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs706549	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs706550	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs706551	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs730884	0.83[ASN][1000 genomes]
rs744514	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7559307	0.96[CHB][hapmap];0.82[ASN][1000 genomes]
rs7574398	0.83[EUR][1000 genomes]
rs7575973	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7585484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7605486	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7605504	0.97[ASN][1000 genomes]
rs782569	0.82[ASN][1000 genomes]
rs782574	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs782580	0.96[CHB][hapmap];0.82[JPT][hapmap]
rs782583	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs782589	0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs782591	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs782593	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs782597	0.90[ASN][1000 genomes]
rs782598	0.94[ASN][1000 genomes]
rs782603	0.92[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs782612	0.95[ASN][1000 genomes]
rs782614	0.82[ASN][1000 genomes]
rs782620	0.96[CHB][hapmap];0.81[JPT][hapmap]
rs782621	0.86[CHB][hapmap]
rs782628	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs782636	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs782647	0.84[ASN][1000 genomes]
rs782648	0.90[ASN][1000 genomes]
rs782651	0.90[ASN][1000 genomes]
rs9636439	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[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	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
rs6545505	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	chr2:55747800-55784000	Weak transcription	Esophagus	oesophagus
2	chr2:55748000-55761200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:55748000-55761200	Weak transcription	Primary B cells from cord blood	blood
4	chr2:55748000-55784000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:55748000-55788000	Weak transcription	Colonic Mucosa	Colon
6	chr2:55748000-55793800	Weak transcription	Psoas Muscle	Psoas
7	chr2:55748200-55764600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr2:55748200-55764600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:55748200-55765000	Weak transcription	K562	blood
10	chr2:55748200-55769600	Weak transcription	Small Intestine	intestine
11	chr2:55748200-55769600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr2:55748200-55772000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:55748200-55773000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:55748200-55775800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:55748200-55777400	Weak transcription	NHLF	lung
16	chr2:55748200-55778800	Weak transcription	Fetal Heart	heart
17	chr2:55748200-55782400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:55748400-55761400	Weak transcription	NHEK	skin
19	chr2:55748400-55764400	Weak transcription	GM12878-XiMat	blood
20	chr2:55748400-55772200	Weak transcription	HMEC	breast
21	chr2:55748600-55770000	Weak transcription	Dnd41	blood
22	chr2:55749600-55758800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:55749600-55760000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:55750000-55775400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:55750400-55760400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:55750600-55760200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:55750800-55759400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:55751000-55759200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:55751000-55759200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:55751000-55759200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr2:55751200-55759400	Strong transcription	Fetal Stomach	stomach
32	chr2:55751400-55764200	Weak transcription	HSMM	muscle
33	chr2:55751800-55766600	Weak transcription	Liver	Liver
34	chr2:55752600-55761400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:55752600-55788200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
37	chr2:55753200-55761400	Weak transcription	Right Ventricle	heart
38	chr2:55753200-55772400	Weak transcription	HepG2	liver
39	chr2:55753400-55759400	Strong transcription	Fetal Intestine Large	intestine
40	chr2:55753400-55761400	Weak transcription	Brain Germinal Matrix	brain
41	chr2:55753400-55772200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr2:55753600-55761800	Weak transcription	HSMMtube	muscle
43	chr2:55753600-55786600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:55753800-55761200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:55753800-55761200	Weak transcription	NHDF-Ad	bronchial
46	chr2:55753800-55766200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr2:55753800-55768800	Weak transcription	Placenta	Placenta
48	chr2:55754000-55774600	Weak transcription	Spleen	Spleen
49	chr2:55754000-55784000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:55754200-55772400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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