Variant report

Variant	rs16961730
Chromosome Location	chr17:17350504-17350505
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17289655..17293959-chr17:17349314..17352438,5	MCF-7	breast:
2	chr17:17348389..17350727-chr17:17740115..17741953,2	MCF-7	breast:
3	chr17:17260627..17264124-chr17:17347628..17351557,3	MCF-7	breast:
4	chr17:17341170..17345071-chr17:17347034..17351413,6	MCF-7	breast:
5	chr17:17348329..17350736-chr18:19191275..19193632,2	MCF-7	breast:
6	chr17:17345336..17348353-chr17:17348575..17352300,3	K562	blood:
7	chr17:17265082..17270324-chr17:17346925..17351276,6	MCF-7	breast:
8	chr17:17344282..17356772-chr17:17394630..17405312,31	MCF-7	breast:
9	chr17:17342531..17346072-chr17:17347773..17351460,6	MCF-7	breast:
10	chr17:17349350..17351226-chr17:17382738..17384846,2	K562	blood:
11	chr17:17335195..17342131-chr17:17347291..17351486,7	MCF-7	breast:
12	chr17:17346012..17348708-chr17:17349032..17351296,2	MCF-7	breast:
13	chr17:17257302..17260550-chr17:17346867..17350783,4	MCF-7	breast:
14	chr17:17348675..17350534-chr17:17351603..17353201,2	MCF-7	breast:
15	chr17:17340093..17354118-chr17:17394085..17402192,31	MCF-7	breast:
16	chr17:17347016..17350522-chr17:17380134..17385375,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000141026	Chromatin interaction
ENSG00000108551	Chromatin interaction
ENSG00000072310	Chromatin interaction
ENSG00000167088	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11869417	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11869428	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1242479	0.83[CEU][hapmap]
rs1242480	0.83[CEU][hapmap]
rs1242482	0.82[CEU][hapmap]
rs1242485	0.86[CEU][hapmap]
rs1242486	0.87[CEU][hapmap]
rs1242488	0.83[CEU][hapmap]
rs1569043	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1969488	0.86[AMR][1000 genomes]
rs35649200	0.82[ASN][1000 genomes]
rs4924853	0.87[AMR][1000 genomes]
rs57000611	0.87[ASN][1000 genomes]
rs7223163	0.82[ASN][1000 genomes]
rs73978916	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73978919	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs906405	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[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	nsv482648	chr17:17315268-17455442	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1065710	chr17:17328111-17391443	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv907729	chr17:17338536-17425279	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17344800-17353400	Weak transcription	Brain Germinal Matrix	brain
2	chr17:17346800-17352200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr17:17348200-17351000	Flanking Active TSS	HepG2	liver
4	chr17:17348200-17351400	Enhancers	Adipose Nuclei	Adipose
5	chr17:17348200-17351400	Enhancers	Fetal Thymus	thymus
6	chr17:17348200-17351800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr17:17348400-17350600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr17:17348400-17351600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr17:17348400-17352000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr17:17348600-17351600	Enhancers	NH-A	brain
11	chr17:17348800-17350600	Enhancers	Stomach Mucosa	stomach
12	chr17:17348800-17350600	Enhancers	NHDF-Ad	bronchial
13	chr17:17348800-17351000	Enhancers	Lung	lung
14	chr17:17348800-17351400	Enhancers	Liver	Liver
15	chr17:17349200-17350600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr17:17349200-17352200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr17:17349600-17363200	Weak transcription	Right Atrium	heart
18	chr17:17349800-17350800	Enhancers	Pancreas	Pancrea
19	chr17:17350000-17350600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:17350000-17350800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr17:17350000-17351800	Enhancers	HUVEC	blood vessel
22	chr17:17350200-17350800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr17:17350200-17351200	Weak transcription	HSMM	muscle
24	chr17:17350400-17350800	Weak transcription	Osteobl	bone
25	chr17:17350400-17351000	Enhancers	A549	lung
26	chr17:17350400-17351200	Weak transcription	Spleen	Spleen
27	chr17:17350400-17351600	Enhancers	Hela-S3	cervix
28	chr17:17350400-17353800	Weak transcription	Fetal Muscle Leg	muscle
29	chr17:17350400-17363400	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links