Variant report

Variant	rs60156243
Chromosome Location	chr1:85706839-85706840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85410308..85411228-chr1:85705720..85706844,7	MCF-7	breast:
2	chr1:85666584..85668196-chr1:85704539..85707139,2	MCF-7	breast:
3	chr1:85694538..85697394-chr1:85706640..85709318,2	MCF-7	breast:
4	chr1:85706037..85709032-chr1:85723528..85726746,4	K562	blood:

Variant related genes	Relation type
ENSG00000097096	Chromatin interaction
ENSG00000162642	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11161556	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11161574	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11161584	0.89[EUR][1000 genomes]
rs11577656	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11583836	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12563295	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17123650	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2252408	0.93[EUR][1000 genomes]
rs2735593	0.93[EUR][1000 genomes]
rs2735594	0.93[EUR][1000 genomes]
rs36006436	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949892	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949926	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6663690	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671589	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693365	0.91[EUR][1000 genomes]
rs709790	0.81[ASN][1000 genomes]
rs72722613	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72722616	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72722624	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72722631	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72722638	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72722641	0.98[ASN][1000 genomes]
rs72722643	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7366220	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60156243	C1orf52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85687000-85709600	Weak transcription	Aorta	Aorta
2	chr1:85705200-85707800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:85705400-85707200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:85705600-85707000	Enhancers	Colon Smooth Muscle	Colon
5	chr1:85705600-85707000	Enhancers	Osteobl	bone
6	chr1:85705600-85707200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:85705600-85707200	Enhancers	Fetal Lung	lung
8	chr1:85705600-85707800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:85705800-85707000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:85705800-85707000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:85705800-85707000	Enhancers	Rectal Smooth Muscle	rectum
12	chr1:85705800-85707000	Enhancers	Stomach Smooth Muscle	stomach
13	chr1:85705800-85707200	Enhancers	HSMMtube	muscle
14	chr1:85706000-85707000	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr1:85706000-85707000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr1:85706000-85707000	Enhancers	Stomach Mucosa	stomach
17	chr1:85706000-85707200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr1:85706000-85707400	Enhancers	Fetal Stomach	stomach
19	chr1:85706000-85709000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:85706000-85716000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:85706200-85707000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:85706200-85707000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr1:85706200-85707000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr1:85706200-85707000	Enhancers	Muscle Satellite Cultured Cells	--
25	chr1:85706200-85707000	Weak transcription	Lung	lung
26	chr1:85706200-85707200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr1:85706200-85707200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:85706200-85707200	Enhancers	HUVEC	blood vessel
29	chr1:85706200-85707800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:85706400-85707000	Enhancers	Primary hematopoietic stem cells	blood
31	chr1:85706400-85707000	Enhancers	HepG2	liver
32	chr1:85706400-85707200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:85706400-85707200	Enhancers	Dnd41	blood
34	chr1:85706400-85709800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:85706400-85710000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:85706400-85710000	Weak transcription	NH-A	brain
37	chr1:85706600-85709200	Weak transcription	Fetal Heart	heart
38	chr1:85706600-85709200	Weak transcription	HSMM	muscle
39	chr1:85706600-85710400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:85706600-85716000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:85706600-85716000	Weak transcription	Fetal Intestine Large	intestine
42	chr1:85706600-85716400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:85706800-85707200	Enhancers	Primary T cells fromperipheralblood	blood
44	chr1:85706800-85707800	Enhancers	Pancreas	Pancrea
45	chr1:85706800-85709000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:85706800-85709000	Weak transcription	Adipose Nuclei	Adipose
47	chr1:85706800-85710000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:85706800-85716000	Weak transcription	Primary T cells from cord blood	blood
49	chr1:85706800-85718400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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