Variant report

Variant	rs1565287
Chromosome Location	chr2:179735946-179735947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179735407..179736123-chr2:179756219..179756764,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10165177	1.00[ASW][hapmap];0.93[CEU][hapmap];0.97[GIH][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10497526	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10803920	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884950	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12469367	1.00[CHB][hapmap]
rs12693171	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1489483	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1489486	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2291306	1.00[CHD][hapmap]
rs4637162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894054	1.00[ASW][hapmap];0.86[LWK][hapmap];0.80[MKK][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes]
rs4894055	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]
rs4894057	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894060	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56345539	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433738	0.87[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6707222	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6734390	0.87[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747791	1.00[JPT][hapmap]
rs7570928	0.93[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573700	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv875455	chr2:179732845-179909467	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1565287	CCDC141	cis	cerebellum	SCAN
rs1565287	FKBP7	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179695800-179738400	Weak transcription	Fetal Intestine Large	intestine
2	chr2:179702200-179749200	Weak transcription	Thymus	Thymus
3	chr2:179710800-179782800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr2:179713400-179778600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:179717000-179790600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr2:179728200-179753800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:179728800-179739600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:179729200-179749000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:179729400-179753600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:179729600-179739400	Weak transcription	Aorta	Aorta
11	chr2:179729600-179747200	Weak transcription	Adipose Nuclei	Adipose
12	chr2:179730600-179739400	Weak transcription	Pancreas	Pancrea
13	chr2:179730600-179739600	Weak transcription	Right Atrium	heart
14	chr2:179730600-179745800	Weak transcription	NHLF	lung
15	chr2:179730600-179749000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:179730800-179745200	Weak transcription	Primary B cells from cord blood	blood
17	chr2:179730800-179750600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:179730800-179756000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:179730800-179770800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr2:179732000-179745200	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:179733000-179736000	Enhancers	HSMMtube	muscle
22	chr2:179733200-179736800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:179733200-179779200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr2:179733400-179736600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:179733800-179754200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:179734200-179736600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr2:179734800-179736000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:179735000-179736000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr2:179735000-179736200	Enhancers	HUVEC	blood vessel
30	chr2:179735000-179736400	Enhancers	HMEC	breast
31	chr2:179735000-179736600	Genic enhancers	Fetal Heart	heart
32	chr2:179735200-179737000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:179735200-179737800	Strong transcription	Primary T cells from cord blood	blood
34	chr2:179735400-179760800	Weak transcription	Right Ventricle	heart
35	chr2:179735800-179738200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:179735800-179738400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:179735800-179738400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:179735800-179738400	Weak transcription	NHEK	skin
39	chr2:179735800-179738600	Weak transcription	Psoas Muscle	Psoas
40	chr2:179735800-179739400	Weak transcription	Left Ventricle	heart
41	chr2:179735800-179739400	Weak transcription	HSMM	muscle

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