Variant report

Variant	rs4894055
Chromosome Location	chr2:179714675-179714676
allele	C/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	STAT3	chr2:179714612-179714960	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
CCDC141	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10165177	1.00[ASW][hapmap];0.87[CEU][hapmap];0.97[GIH][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10497526	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10803920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884950	0.95[EUR][1000 genomes]
rs12469367	1.00[CHB][hapmap]
rs12693171	0.93[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs1489483	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1489486	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1565287	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17362588	0.81[CEU][hapmap];0.88[MEX][hapmap]
rs2291306	1.00[CHD][hapmap]
rs4637162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894054	1.00[ASW][hapmap];0.81[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4894057	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894060	0.93[EUR][1000 genomes]
rs56345539	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433738	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6707222	0.93[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs6734390	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747791	1.00[JPT][hapmap]
rs7570928	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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	nsv834470	chr2:179555152-179728726	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv934108	chr2:179556852-179729925	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4894055	CCDC141	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179693400-179726000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:179695800-179738400	Weak transcription	Fetal Intestine Large	intestine
3	chr2:179696400-179728800	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr2:179702200-179749200	Weak transcription	Thymus	Thymus
5	chr2:179702400-179729200	Weak transcription	Lung	lung
6	chr2:179702400-179730000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:179702800-179728600	Weak transcription	Pancreas	Pancrea
8	chr2:179704400-179720800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:179707200-179721000	Strong transcription	Primary T cells from cord blood	blood
10	chr2:179708000-179727800	Weak transcription	Psoas Muscle	Psoas
11	chr2:179709400-179714800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:179710200-179715000	Weak transcription	Ovary	ovary
13	chr2:179710800-179722400	Weak transcription	Fetal Lung	lung
14	chr2:179710800-179724000	Weak transcription	Fetal Intestine Small	intestine
15	chr2:179710800-179782800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:179711200-179715000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:179711400-179714800	Weak transcription	Fetal Brain Male	brain
18	chr2:179711400-179719400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:179711400-179720600	Weak transcription	Right Ventricle	heart
20	chr2:179711600-179719800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:179711600-179723800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:179711600-179728000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:179711600-179728400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:179712000-179719200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:179712000-179727000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:179712200-179725800	Weak transcription	Left Ventricle	heart
27	chr2:179712600-179718200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:179713000-179721400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:179713000-179724400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:179713200-179716800	Weak transcription	Fetal Heart	heart
31	chr2:179713400-179715200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:179713400-179715200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:179713400-179716200	Weak transcription	Primary B cells from cord blood	blood
34	chr2:179713400-179722800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:179713400-179729200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr2:179713400-179778600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:179714000-179723800	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:179714200-179716000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:179714200-179716000	Weak transcription	HSMMtube	muscle
40	chr2:179714600-179716200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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