Variant report

Variant	rs706548
Chromosome Location	chr2:55850106-55850107
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55843280..55846696-chr2:55847912..55852861,6	MCF-7	breast:
2	chr2:55848892..55851384-chr2:55854717..55856988,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138041	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10460508	0.85[CEU][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap]
rs10496050	0.89[CEU][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap]
rs1058582	0.87[ASN][1000 genomes]
rs1084522	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs1084525	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs11125581	0.86[ASN][1000 genomes]
rs17278044	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17369191	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1823893	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs1975484	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs1975487	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs2586947	0.93[ASN][1000 genomes]
rs2586950	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2586954	0.85[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap]
rs2627759	0.95[ASN][1000 genomes]
rs2627773	0.83[JPT][hapmap]
rs2627775	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]
rs2627776	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs35504023	0.89[CEU][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap]
rs3762513	0.85[ASN][1000 genomes]
rs4290693	0.89[CEU][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap]
rs4672052	0.83[CEU][hapmap]
rs4672054	0.85[ASN][1000 genomes]
rs55761024	0.87[ASN][1000 genomes]
rs62165181	0.85[ASN][1000 genomes]
rs6545506	0.89[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs7582278	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs782568	0.85[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap]
rs782572	0.83[JPT][hapmap]
rs782573	0.83[JPT][hapmap]
rs782584	1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs782586	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs782587	0.95[ASN][1000 genomes]
rs782588	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs782590	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs782594	0.95[ASN][1000 genomes]
rs782595	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs782599	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs782600	0.95[ASN][1000 genomes]
rs782601	0.95[ASN][1000 genomes]
rs782602	1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs782606	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs782629	0.82[GIH][hapmap];0.90[JPT][hapmap]
rs782630	0.82[JPT][hapmap]
rs782634	0.83[JPT][hapmap]
rs782637	0.82[GIH][hapmap];0.83[JPT][hapmap]
rs782649	0.93[ASN][1000 genomes]
rs782650	0.90[ASN][1000 genomes]
rs782652	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs809732	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs706548	SMEK2	cis	parietal	SCAN
rs706548	CCDC104	cis	parietal	SCAN
rs706548	PNPT1	Cis_1M	lymphoblastoid	RTeQTL
rs706548	POMC	trans	lymphoblastoid	seeQTL
rs706548	PNPT1	cis	cerebellum	SCAN
rs706548	CCDC104	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846400-55870000	Weak transcription	Aorta	Aorta
2	chr2:55846600-55850400	Genic enhancers	Primary T cells fromperipheralblood	blood
3	chr2:55846600-55851600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:55846600-55852000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr2:55846600-55859400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:55846600-55861800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:55846600-55862200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:55846600-55862800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:55846600-55863400	Weak transcription	Fetal Kidney	kidney
10	chr2:55846600-55870000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:55846600-55870000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:55846800-55850400	Enhancers	Liver	Liver
13	chr2:55846800-55851200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr2:55846800-55853000	Weak transcription	A549	lung
15	chr2:55846800-55858200	Weak transcription	HSMM	muscle
16	chr2:55846800-55862000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:55846800-55862000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:55846800-55862200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:55846800-55862600	Weak transcription	NHDF-Ad	bronchial
20	chr2:55846800-55863400	Weak transcription	HSMMtube	muscle
21	chr2:55846800-55863400	Weak transcription	NHLF	lung
22	chr2:55846800-55863800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:55847000-55852600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr2:55847400-55852400	Weak transcription	HMEC	breast
26	chr2:55847400-55852800	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr2:55847400-55859400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:55847400-55862200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:55847600-55850200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:55847600-55852400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:55847600-55852600	Weak transcription	Brain Anterior Caudate	brain
33	chr2:55847600-55852600	Weak transcription	Right Atrium	heart
34	chr2:55847600-55857400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:55847600-55860800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:55847600-55862000	Weak transcription	Osteobl	bone
37	chr2:55847600-55864200	Weak transcription	Brain Germinal Matrix	brain
38	chr2:55847600-55870000	Weak transcription	Colonic Mucosa	Colon
39	chr2:55847600-55870000	Weak transcription	Psoas Muscle	Psoas
40	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
41	chr2:55847800-55850400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:55847800-55850400	Genic enhancers	Dnd41	blood
43	chr2:55847800-55850600	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr2:55847800-55852400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:55847800-55852400	Weak transcription	NHEK	skin
46	chr2:55847800-55852600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:55847800-55859000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:55847800-55862000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr2:55847800-55862000	Weak transcription	NH-A	brain
50	chr2:55847800-55862200	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links