Variant report

Variant	rs1009570
Chromosome Location	chr17:38596425-38596426
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	CTCF	chr17:38596280-38596430	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38573492..38575865-chr17:38596037..38598385,2	K562	blood:
2	chr17:38456433..38460322-chr17:38596356..38599161,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240125	TF binding region
IGFBP4	TF binding region
ENSG00000131747	Chromatin interaction
ENSG00000270145	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10852940	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11078945	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11657212	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16965783	1.00[YRI][hapmap]
rs1868758	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015561	0.90[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35103116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4890114	0.81[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs56394376	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs584438	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs584828	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs598892	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs632224	0.93[EUR][1000 genomes];0.99[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	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv908223	chr17:38530799-38609187	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv960101	chr17:38594067-38597269	Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1009570	MMP28	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38579600-38598800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr17:38584600-38600200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr17:38589600-38598800	Weak transcription	Fetal Intestine Small	intestine
4	chr17:38589800-38598600	Weak transcription	NHDF-Ad	bronchial
5	chr17:38590200-38599000	Weak transcription	Lung	lung
6	chr17:38590400-38597400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr17:38590400-38598600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:38590400-38598800	Weak transcription	Osteobl	bone
9	chr17:38590600-38596600	Weak transcription	A549	lung
10	chr17:38593200-38598800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr17:38593600-38598800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr17:38593800-38597400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr17:38593800-38598600	Weak transcription	HUVEC	blood vessel
14	chr17:38594000-38597200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr17:38594000-38597400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr17:38594000-38597400	Weak transcription	Liver	Liver
17	chr17:38594000-38598600	Weak transcription	Placenta	Placenta
18	chr17:38594000-38598800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr17:38594000-38598800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr17:38594000-38598800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr17:38594000-38598800	Weak transcription	Fetal Lung	lung
22	chr17:38594000-38598800	Weak transcription	HMEC	breast
23	chr17:38594000-38598800	Weak transcription	NHLF	lung
24	chr17:38594000-38599000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr17:38594200-38596600	Weak transcription	Spleen	Spleen
26	chr17:38594200-38597400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr17:38594200-38597400	Weak transcription	Colon Smooth Muscle	Colon
28	chr17:38594200-38597400	Weak transcription	Fetal Muscle Leg	muscle
29	chr17:38594200-38597400	Weak transcription	Right Ventricle	heart
30	chr17:38594200-38598600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr17:38594200-38598600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr17:38594200-38598600	Weak transcription	Right Atrium	heart
33	chr17:38594200-38598800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr17:38594200-38598800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr17:38594200-38598800	Weak transcription	Esophagus	oesophagus
36	chr17:38594200-38598800	Weak transcription	Left Ventricle	heart
37	chr17:38594200-38598800	Weak transcription	Dnd41	blood
38	chr17:38594200-38599000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr17:38594200-38599000	Weak transcription	HSMM	muscle
40	chr17:38594400-38597400	Weak transcription	Adipose Nuclei	Adipose
41	chr17:38594400-38597400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr17:38594400-38597400	Weak transcription	K562	blood
43	chr17:38594400-38597600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr17:38594600-38598800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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