Variant report

Variant	rs6675105
Chromosome Location	chr1:78510544-78510545
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr1:78510531-78510708	GM12891	blood:	n/a	n/a
2	NFIC	chr1:78510309-78510766	GM12878	blood:	n/a	n/a
3	SUZ12	chr1:78510446-78512858	NT2-D1	testis:	n/a	n/a
4	MAFF	chr1:78510426-78511041	HepG2	liver:	n/a	n/a
5	MAFK	chr1:78510544-78511120	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000213561	TF binding region
GIPC2	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1039863	1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10735751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10873962	0.95[ASN][1000 genomes]
rs10873963	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1166696	0.82[ASN][1000 genomes]
rs1166699	0.82[ASN][1000 genomes]
rs1166700	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs11811805	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1510244	0.85[ASN][1000 genomes]
rs1749911	0.80[ASN][1000 genomes]
rs1749913	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1780044	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1780045	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1780047	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1780048	0.82[ASN][1000 genomes]
rs2296452	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap]
rs2296454	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap]
rs3736909	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3767024	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap]
rs3767025	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3790586	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4083559	0.81[ASN][1000 genomes]
rs4107671	0.85[ASN][1000 genomes]
rs4483454	0.82[ASN][1000 genomes]
rs4543852	0.85[ASN][1000 genomes]
rs4631748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6424648	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap]
rs6424653	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6680447	0.85[ASN][1000 genomes]
rs6699513	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6702465	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap]
rs7520255	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7524504	0.85[ASN][1000 genomes]
rs7547599	0.83[CHB][hapmap]
rs9661687	0.81[ASN][1000 genomes]
rs9662129	0.93[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9729146	0.93[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.82[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	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6675105	C1orf173	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78505000-78511000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:78506800-78510800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:78508600-78511000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:78509200-78510600	Enhancers	Liver	Liver
5	chr1:78509200-78511000	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr1:78509400-78511000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr1:78509600-78510600	Enhancers	Adipose Nuclei	Adipose
8	chr1:78509800-78511000	Active TSS	Duodenum Mucosa	Duodenum
9	chr1:78509800-78511200	Weak transcription	HSMM	muscle
10	chr1:78510000-78513200	Active TSS	Pancreas	Pancrea
11	chr1:78510200-78510600	Enhancers	HepG2	liver
12	chr1:78510200-78511800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr1:78510400-78510600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
14	chr1:78510400-78510600	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
15	chr1:78510400-78510600	Flanking Active TSS	Fetal Intestine Large	intestine
16	chr1:78510400-78510600	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr1:78510400-78510600	Enhancers	Right Ventricle	heart
18	chr1:78510400-78510800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
19	chr1:78510400-78510800	Flanking Active TSS	Fetal Intestine Small	intestine
20	chr1:78510400-78511600	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
21	chr1:78510400-78512800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:78510400-78513000	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr1:78510400-78513800	Flanking Active TSS	HUVEC	blood vessel

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