Variant report

Variant	rs3866675
Chromosome Location	chr17:38681514-38681515
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr17:38681460-38682017	K562	blood:	n/a	n/a
2	CBX3	chr17:38681493-38681977	K562	blood:	n/a	n/a
3	USF1	chr17:38681497-38681934	K562	blood:	n/a	n/a
4	CEBPB	chr17:38681408-38682046	A549	lung:	n/a	chr17:38681737-38681748
5	SETDB1	chr17:38681402-38682100	U2OS	brain:	n/a	n/a
6	TRIM28	chr17:38681446-38681964	K562	blood:	n/a	n/a
7	KAP1	chr17:38681344-38682527	K562	blood:	n/a	n/a
8	JUN	chr17:38681455-38682038	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38474075..38478371-chr17:38679567..38683859,4	MCF-7	breast:
2	chr17:38676381..38678576-chr17:38679743..38681770,2	K562	blood:
3	chr17:38675352..38677497-chr17:38677864..38681564,3	MCF-7	breast:
4	chr17:38673127..38676333-chr17:38678075..38682047,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000266088	TF binding region
ENSG00000266088	Chromatin interaction
ENSG00000131759	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1072070	0.87[EUR][1000 genomes]
rs11871009	1.00[EUR][1000 genomes]
rs16965857	1.00[EUR][1000 genomes]
rs16965864	1.00[EUR][1000 genomes]
rs16965890	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28485796	1.00[EUR][1000 genomes]
rs56151683	1.00[EUR][1000 genomes]
rs7208120	1.00[EUR][1000 genomes]
rs7222478	1.00[EUR][1000 genomes]
rs8064741	1.00[EUR][1000 genomes]
rs8064890	1.00[EUR][1000 genomes]
rs8065657	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9894865	1.00[EUR][1000 genomes]
rs9899509	1.00[EUR][1000 genomes]
rs9905376	0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9909468	1.00[EUR][1000 genomes]
rs9910719	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9915820	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058185	chr17:38629339-38689908	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38675600-38686600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr17:38677600-38682200	Weak transcription	Spleen	Spleen
3	chr17:38677600-38687800	Weak transcription	Right Ventricle	heart
4	chr17:38678000-38683000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:38678000-38686800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:38678200-38684200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr17:38678200-38685200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr17:38678600-38681800	Weak transcription	HSMM	muscle
9	chr17:38678600-38684200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr17:38678800-38686800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr17:38679000-38682800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr17:38679200-38684200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr17:38679200-38686600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr17:38679200-38686800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr17:38679400-38681600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr17:38679600-38683400	ZNF genes & repeats	A549	lung
17	chr17:38679800-38682000	ZNF genes & repeats	Primary B cells from cord blood	blood
18	chr17:38679800-38683000	Weak transcription	Esophagus	oesophagus
19	chr17:38680000-38681800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr17:38680000-38685600	Weak transcription	Hela-S3	cervix
21	chr17:38680400-38682000	ZNF genes & repeats	Dnd41	blood
22	chr17:38680800-38682000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr17:38680800-38686400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr17:38681000-38682400	Weak transcription	Placenta	Placenta
25	chr17:38681000-38686800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr17:38681200-38682400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr17:38681200-38682400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr17:38681200-38682800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr17:38681200-38686600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr17:38681200-38688600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr17:38681400-38681600	Weak transcription	HepG2	liver
32	chr17:38681400-38681800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links