Variant report

Variant	rs9944423
Chromosome Location	chr17:17484934-17484935
allele	A/G
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	ESR1	chr17:17484834-17485234	ECC-1	luminal epithelium:	n/a	chr17:17485048-17485063 chr17:17485048-17485065
2	CEBPB	chr17:17484803-17485003	HepG2	liver:	n/a	n/a
3	ESR1	chr17:17484772-17485198	ECC-1	luminal epithelium:	n/a	chr17:17485048-17485063 chr17:17485048-17485065
4	FOSL2	chr17:17484894-17485328	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17481596..17485305-chr17:17490709..17495159,5	MCF-7	breast:

Variant related genes	Relation type
PEMT	TF binding region
ENSG00000264666	Chromatin interaction
ENSG00000133027	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10401038	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11651280	0.83[EUR][1000 genomes]
rs11651378	1.00[CEU][hapmap]
rs11651957	0.85[EUR][1000 genomes]
rs11654553	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11654777	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11658311	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11658944	1.00[CEU][hapmap]
rs11659047	1.00[CEU][hapmap]
rs13342397	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16961845	1.00[AMR][1000 genomes]
rs28454257	0.83[EUR][1000 genomes]
rs28583584	1.00[EUR][1000 genomes]
rs28636952	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28652618	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28715719	0.83[EUR][1000 genomes]
rs28884183	0.83[EUR][1000 genomes]
rs35301480	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35838363	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56030759	0.98[EUR][1000 genomes]
rs56044345	0.83[EUR][1000 genomes]
rs56177028	0.83[EUR][1000 genomes]
rs56327101	0.83[EUR][1000 genomes]
rs57638011	0.83[EUR][1000 genomes]
rs58729290	0.80[AMR][1000 genomes]
rs60831194	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7210978	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7214152	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7214988	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7215055	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7216223	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7217764	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7219568	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7222358	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7222759	0.81[EUR][1000 genomes]
rs7224725	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7225421	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73978969	1.00[AMR][1000 genomes]
rs73978990	0.87[EUR][1000 genomes]
rs8064558	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs8070432	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8071007	0.87[EUR][1000 genomes]
rs8074742	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8074981	0.83[EUR][1000 genomes]
rs8076601	0.83[EUR][1000 genomes]
rs8077671	0.83[EUR][1000 genomes]
rs8081961	1.00[AMR][1000 genomes]
rs897456	1.00[CEU][hapmap]
rs9889584	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9889795	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9890062	0.82[AMR][1000 genomes]
rs9896285	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9897362	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9903468	0.91[AMR][1000 genomes]
rs9903503	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9904004	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9905032	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9905191	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9910151	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9910747	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9911823	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9914118	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907731	chr17:17358004-17504856	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv907744	chr17:17404586-17504856	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv907747	chr17:17412032-17504856	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv470579	chr17:17424332-17493810	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
8	nsv1062052	chr17:17461050-17507199	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv543237	chr17:17461050-17507199	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv833383	chr17:17464635-17509138	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17469000-17494000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:17469200-17493600	Weak transcription	Thymus	Thymus
3	chr17:17471600-17493600	Weak transcription	Brain Angular Gyrus	brain
4	chr17:17471800-17493600	Weak transcription	Colon Smooth Muscle	Colon
5	chr17:17472400-17493600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr17:17474200-17493600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr17:17474600-17493800	Weak transcription	Primary B cells from cord blood	blood
8	chr17:17474800-17493200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:17478200-17493800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr17:17479800-17493400	Weak transcription	HMEC	breast
11	chr17:17480200-17490800	Weak transcription	NHEK	skin
12	chr17:17480200-17493000	Weak transcription	Brain Germinal Matrix	brain
13	chr17:17480200-17493600	Weak transcription	Esophagus	oesophagus
14	chr17:17480200-17493600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr17:17480400-17485000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr17:17480400-17487200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr17:17480400-17492800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr17:17480400-17493400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr17:17480400-17493400	Weak transcription	Pancreas	Pancrea
20	chr17:17480400-17493600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr17:17480400-17493600	Weak transcription	Fetal Brain Female	brain
22	chr17:17480400-17493600	Weak transcription	Left Ventricle	heart
23	chr17:17480400-17493600	Weak transcription	Spleen	Spleen
24	chr17:17480400-17493600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr17:17480400-17493800	Weak transcription	Primary T cells from cord blood	blood
26	chr17:17480400-17493800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr17:17480400-17493800	Weak transcription	Colonic Mucosa	Colon
28	chr17:17480600-17485000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr17:17480600-17486800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr17:17480600-17487400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr17:17480600-17492000	Weak transcription	Dnd41	blood
32	chr17:17480600-17493000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr17:17480600-17493400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr17:17480600-17493400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr17:17480600-17493400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr17:17480600-17493600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr17:17480600-17493600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr17:17480600-17493600	Weak transcription	NHLF	lung
39	chr17:17480800-17485600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr17:17480800-17486000	Weak transcription	Brain Anterior Caudate	brain
41	chr17:17480800-17493200	Weak transcription	Lung	lung
42	chr17:17480800-17493800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr17:17481000-17494000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr17:17483000-17485400	Enhancers	Placenta	Placenta
45	chr17:17483000-17485800	Enhancers	Fetal Muscle Leg	muscle
46	chr17:17483000-17486200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr17:17483000-17486400	Enhancers	Adipose Nuclei	Adipose
48	chr17:17483200-17485800	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr17:17483200-17486200	Enhancers	Fetal Intestine Large	intestine
50	chr17:17483400-17485200	Flanking Active TSS	Liver	Liver

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