Variant report

Variant	rs17428174
Chromosome Location	chr2:172886148-172886149
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr2:172886102-172886267	K562	blood:	n/a	n/a
2	KAP1	chr2:172886046-172887342	U2OS	brain:	n/a	n/a
3	SPI1	chr2:172886033-172886292	HL-60	blood:	n/a	n/a
4	KAP1	chr2:172886041-172887303	HEK293	kidney:	n/a	n/a
5	SPI1	chr2:172885960-172886373	HL-60	blood:	n/a	n/a
6	ATF1	chr2:172886054-172886409	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:172884857..172888115-chr2:172946694..172951424,5	K562	blood:
2	chr2:172885280..172887924-chr2:172947289..172951692,6	MCF-7	breast:
3	chr2:172874695..172877681-chr2:172884146..172886439,2	K562	blood:

No data

Variant related genes	Relation type
METAP1D	TF binding region
ENSG00000144355	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1008152	0.88[AMR][1000 genomes]
rs12622895	0.85[CEU][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs17428076	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs17500114	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3736499	0.84[CEU][hapmap];0.91[TSI][hapmap]
rs3765166	0.85[CEU][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs3770448	0.85[TSI][hapmap]
rs3796058	0.85[MEX][hapmap]
rs3821093	0.83[CEU][hapmap]
rs55863868	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56218609	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62183804	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183808	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183809	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183811	0.80[AMR][1000 genomes]
rs62183852	0.88[AMR][1000 genomes]
rs6704590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737876	0.88[AMR][1000 genomes]
rs6749895	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72892835	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72892859	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs788161	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs788164	0.85[CEU][hapmap]
rs788168	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172865200-172886600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:172865600-172897400	Weak transcription	Primary T cells from cord blood	blood
3	chr2:172865800-172886400	Weak transcription	Fetal Intestine Small	intestine
4	chr2:172865800-172886600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:172866000-172886800	Weak transcription	HSMMtube	muscle
6	chr2:172874200-172886400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:172878200-172886400	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:172878600-172886400	Weak transcription	Ovary	ovary
9	chr2:172878600-172886600	Weak transcription	Psoas Muscle	Psoas
10	chr2:172878600-172898200	Weak transcription	Primary B cells from cord blood	blood
11	chr2:172878800-172886600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:172882000-172886800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:172883400-172886200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:172883400-172886200	Weak transcription	K562	blood
15	chr2:172883800-172887200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:172884200-172886600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:172885200-172886600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:172885400-172886200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:172885600-172886200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:172886000-172886200	Enhancers	A549	lung
21	chr2:172886000-172886400	Enhancers	HepG2	liver
22	chr2:172886000-172886400	Enhancers	Osteobl	bone
23	chr2:172886000-172886800	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr2:172886000-172887200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:172886000-172887200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr2:172886000-172887400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr2:172886000-172887600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr2:172886000-172887600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links