Variant report

Variant	rs9901908
Chromosome Location	chr17:38655715-38655716
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38597908..38601053-chr17:38654458..38659532,5	MCF-7	breast:
2	chr17:38654631..38657600-chr17:38717597..38719399,2	MCF-7	breast:
3	chr17:38653160..38655925-chr17:38703995..38706258,2	MCF-7	breast:
4	chr17:38653701..38656623-chr17:38703547..38705327,2	MCF-7	breast:
5	chr17:38650172..38654327-chr17:38654681..38657235,5	K562	blood:
6	chr17:38652390..38654327-chr17:38654701..38657049,2	K562	blood:

Variant related genes	Relation type
ENSG00000141753	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1018953	1.00[JPT][hapmap]
rs11574663	1.00[JPT][hapmap]
rs2229095	1.00[JPT][hapmap]
rs28485796	0.88[ASN][1000 genomes]
rs28493507	0.82[AMR][1000 genomes]
rs3136687	1.00[JPT][hapmap]
rs3136689	1.00[JPT][hapmap]
rs3136694	1.00[JPT][hapmap]
rs3136695	1.00[JPT][hapmap]
rs4092050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs475298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890086	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4890087	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs499490	1.00[CHB][hapmap]
rs594783	1.00[CHB][hapmap]
rs596960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs634299	1.00[ASN][1000 genomes]
rs6503543	0.82[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7212543	0.87[YRI][hapmap];0.82[AMR][1000 genomes]
rs7217539	0.82[CEU][hapmap]
rs7219622	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7221799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs896135	0.82[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs896136	0.82[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs921394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9675320	1.00[JPT][hapmap]
rs9895221	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9912358	1.00[JPT][hapmap]

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:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38643800-38656000	Weak transcription	Right Atrium	heart
2	chr17:38647000-38656000	Weak transcription	Lung	lung
3	chr17:38647000-38656200	Weak transcription	Gastric	stomach
4	chr17:38647200-38656000	Weak transcription	Pancreas	Pancrea
5	chr17:38648200-38655800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr17:38649600-38657600	Transcr. at gene 5' and 3'	NHEK	skin
7	chr17:38652800-38656000	Weak transcription	Spleen	Spleen
8	chr17:38653200-38655800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr17:38653600-38656600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr17:38653800-38655800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr17:38653800-38655800	Enhancers	Osteobl	bone
12	chr17:38653800-38656000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:38653800-38656400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr17:38653800-38656800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr17:38653800-38657000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr17:38653800-38657200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:38654200-38655800	Enhancers	Fetal Muscle Trunk	muscle
18	chr17:38654200-38655800	Enhancers	K562	blood
19	chr17:38654200-38656000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr17:38654200-38656600	Enhancers	NHDF-Ad	bronchial
21	chr17:38654200-38656800	Enhancers	Left Ventricle	heart
22	chr17:38654200-38657000	Enhancers	Right Ventricle	heart
23	chr17:38654400-38655800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:38654400-38656000	Enhancers	Fetal Muscle Leg	muscle
25	chr17:38654600-38655800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr17:38654600-38656000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr17:38654800-38655800	Weak transcription	HSMM	muscle
28	chr17:38654800-38656000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr17:38654800-38656000	Active TSS	HMEC	breast
30	chr17:38654800-38658000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr17:38655000-38655800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr17:38655000-38655800	Enhancers	Fetal Intestine Small	intestine
33	chr17:38655000-38656000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr17:38655000-38656000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr17:38655000-38656000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr17:38655000-38656000	Weak transcription	NHLF	lung
37	chr17:38655000-38656400	Enhancers	Primary hematopoietic stem cells	blood
38	chr17:38655200-38656000	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr17:38655200-38656000	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr17:38655200-38656000	Active TSS	A549	lung
41	chr17:38655200-38656200	Active TSS	Hela-S3	cervix
42	chr17:38655400-38655800	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr17:38655400-38656000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr17:38655400-38656000	Enhancers	Stomach Mucosa	stomach
45	chr17:38655400-38656200	Active TSS	Esophagus	oesophagus
46	chr17:38655400-38656400	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr17:38655400-38656600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr17:38655400-38656800	Enhancers	Fetal Heart	heart
49	chr17:38655400-38656800	Flanking Active TSS	Placenta	Placenta
50	chr17:38655600-38655800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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