Variant report

Variant	rs28627663
Chromosome Location	chr17:37999248-37999249
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	RUNX3	chr17:37999188-38000123	GM12878	blood:	n/a	n/a
2	POLR2A	chr17:37999010-37999882	GM12892	blood:	n/a	n/a
3	WRNIP1	chr17:37999224-37999481	GM12878	blood:	n/a	n/a
4	POLR2A	chr17:37999058-37999885	GM12892	blood:	n/a	n/a
5	POLR2A	chr17:37999050-38000115	GM12878	blood:	n/a	n/a
6	NFIC	chr17:37999163-38000191	GM12878	blood:	n/a	n/a
7	POLR2A	chr17:37998979-37999762	GM12892	blood:	n/a	n/a
8	POLR2A	chr17:37999009-38000069	GM12891	blood:	n/a	n/a
9	MTA3	chr17:37999032-38000206	GM12878	blood:	n/a	n/a
10	POLR2A	chr17:37999081-37999588	GM12878	blood:	n/a	n/a
11	NFATC1	chr17:37999165-37999888	GM12878	blood:	n/a	n/a
12	ATF2	chr17:37999211-38000194	GM12878	blood:	n/a	n/a
13	BCLAF1	chr17:37999056-38000188	GM12878	blood:	n/a	n/a
14	POLR2A	chr17:37999110-38000728	GM12891	blood:	n/a	n/a
15	ELK1	chr17:37999044-37999408	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:37993320..37996437-chr17:37998688..38001239,3	K562	blood:
2	chr17:37997862..38000754-chr17:38065312..38067694,2	K562	blood:

Variant related genes	Relation type
ENSG00000226117	TF binding region
ENSG00000226117	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13341681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13380812	1.00[AMR][1000 genomes]
rs28407584	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28409251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28432878	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28433533	0.87[AFR][1000 genomes]
rs28464000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28494476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28498893	1.00[AMR][1000 genomes]
rs28505218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28661251	1.00[AMR][1000 genomes]
rs28673180	1.00[AMR][1000 genomes]
rs28714172	1.00[AMR][1000 genomes]
rs28882824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61737968	1.00[AMR][1000 genomes]
rs62065168	1.00[AMR][1000 genomes]
rs62065210	1.00[AMR][1000 genomes]
rs9890508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9890819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9893628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9893933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9895237	1.00[AMR][1000 genomes]
rs9896961	1.00[AMR][1000 genomes]
rs9897451	1.00[AMR][1000 genomes]
rs9897847	1.00[AMR][1000 genomes]
rs9899977	1.00[AMR][1000 genomes]
rs9900885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9911163	1.00[AMR][1000 genomes]
rs9913746	1.00[AMR][1000 genomes]
rs9914556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9916301	1.00[AMR][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	nsv1064787	chr17:37892843-38054410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv543342	chr17:37892843-38054410	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv1795575	chr17:37974075-38041762	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37996400-38001400	Genic enhancers	Primary B cells from peripheral blood	blood
2	chr17:37996400-38001400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr17:37997000-37999400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr17:37997400-38005000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr17:37997600-37999400	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr17:37997800-37999400	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr17:37997800-38001400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr17:37998200-37999400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr17:37998400-37999400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr17:37998400-37999400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr17:37998600-37999400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
12	chr17:37998600-37999600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr17:37998600-38000800	Enhancers	Thymus	Thymus
14	chr17:37998600-38001000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr17:37998600-38001000	Enhancers	Fetal Thymus	thymus
16	chr17:37998800-37999600	Genic enhancers	Primary B cells from cord blood	blood
17	chr17:37999200-37999400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr17:37999200-37999800	Active TSS	Primary T cells fromperipheralblood	blood
19	chr17:37999200-38000400	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr17:37999200-38000600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links