Variant report

Variant	rs2627776
Chromosome Location	chr2:55873301-55873302
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55867632..55869380-chr2:55872094..55873711,2	K562	blood:
2	chr2:55842502..55844882-chr2:55870584..55873430,2	MCF-7	breast:
3	chr2:55844652..55846516-chr2:55872491..55875236,2	MCF-7	breast:
4	chr2:55872045..55873893-chr2:55874188..55876944,2	K562	blood:

Variant related genes	Relation type
ENSG00000272606	Chromatin interaction
ENSG00000138035	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10165864	0.82[CEU][hapmap]
rs10460508	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10496050	0.96[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1058582	0.82[EUR][1000 genomes]
rs1084522	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1084525	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11125581	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12329050	0.86[YRI][hapmap]
rs17278044	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17369191	0.96[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap]
rs17798852	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1823893	0.96[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1975484	0.96[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1975487	0.92[CEU][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap]
rs2586947	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2586950	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2586952	0.89[AFR][1000 genomes]
rs2586954	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2586968	0.84[AFR][1000 genomes]
rs2586969	0.82[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2586970	0.82[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2627759	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2627765	0.85[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2627766	0.88[AFR][1000 genomes]
rs2627772	0.85[AFR][1000 genomes]
rs2627773	0.86[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2627775	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	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2627779	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2627780	0.82[AFR][1000 genomes]
rs2627782	0.84[AFR][1000 genomes]
rs35504023	0.96[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3762513	0.81[EUR][1000 genomes]
rs4290693	0.96[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4312532	0.83[CEU][hapmap];0.95[YRI][hapmap]
rs4672052	0.91[CEU][hapmap]
rs4672054	0.81[EUR][1000 genomes]
rs4672055	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4672056	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55761024	0.81[EUR][1000 genomes]
rs58003472	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62165181	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62165184	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62165196	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62165197	0.83[EUR][1000 genomes]
rs6545506	0.96[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs706548	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7582278	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7594279	0.87[EUR][1000 genomes]
rs7596377	0.87[YRI][hapmap]
rs782566	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs782567	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs782568	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs782572	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs782573	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs782584	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs782586	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782587	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782588	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782590	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782594	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782595	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs782599	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782600	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782601	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782602	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs782606	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs782629	0.85[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs782630	0.87[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs782632	0.86[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs782633	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs782634	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs782637	0.82[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs782649	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs782650	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs782652	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]
rs809732	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs935177	0.82[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs9917139	0.82[CEU][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2627776	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

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	chr2:55857000-55873800	Strong transcription	Fetal Thymus	thymus
7	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
8	chr2:55858800-55873400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:55858800-55875600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:55858800-55877200	Strong transcription	Dnd41	blood
11	chr2:55859000-55876800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:55859000-55877000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:55859000-55877200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr2:55859200-55874000	Weak transcription	Pancreas	Pancrea
15	chr2:55859400-55875600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:55859400-55877600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:55859800-55873600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
19	chr2:55861800-55875000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:55861800-55875800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr2:55862000-55873400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:55862000-55874800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr2:55862000-55875000	Strong transcription	Fetal Intestine Large	intestine
24	chr2:55862000-55877200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:55862000-55877800	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:55862200-55873800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr2:55862200-55874000	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:55862200-55874400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:55862200-55874800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:55863400-55875600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:55864000-55893200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:55864200-55882800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:55864400-55919600	Weak transcription	NHLF	lung
34	chr2:55864600-55881400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr2:55864600-55881400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr2:55864800-55874800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:55864800-55879200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr2:55865000-55880400	Weak transcription	HMEC	breast
39	chr2:55865600-55873400	Strong transcription	Osteobl	bone
40	chr2:55866200-55873800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr2:55866200-55882400	Weak transcription	Ovary	ovary
42	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr2:55866800-55875000	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr2:55867200-55875000	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr2:55868000-55879200	Weak transcription	NH-A	brain
46	chr2:55868600-55873600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:55868600-55874600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr2:55868800-55874000	Strong transcription	Liver	Liver
49	chr2:55869000-55874000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:55869600-55873600	Weak transcription	HSMMtube	muscle

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