Variant report

Variant	rs17683509
Chromosome Location	chr19:18306990-18306991
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18303093..18307365-chr19:18386584..18393500,10	K562	blood:
2	chr19:18262556..18266763-chr19:18301801..18307197,7	K562	blood:
3	chr19:18302787..18307396-chr19:18383842..18390051,8	K562	blood:
4	chr19:18301873..18308921-chr19:18309874..18315133,13	MCF-7	breast:
5	chr19:18302289..18309850-chr19:18311214..18320810,23	K562	blood:
6	chr19:18283035..18288338-chr19:18301660..18307351,8	K562	blood:
7	chr19:18302057..18307216-chr19:18311605..18315914,14	MCF-7	breast:
8	chr19:18110949..18114806-chr19:18305445..18308231,3	MCF-7	breast:
9	chr19:18268586..18275019-chr19:18302013..18308723,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000105647	Chromatin interaction
ENSG00000216490	Chromatin interaction
ENSG00000267959	Chromatin interaction
ENSG00000268173	Chromatin interaction
ENSG00000268650	Chromatin interaction
ENSG00000105649	Chromatin interaction
ENSG00000130518	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000105643	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1046565	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11881258	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12460619	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12461021	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12462801	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17683539	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2049050	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2229228	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs2241089	0.87[YRI][hapmap]
rs2241090	0.87[YRI][hapmap]
rs2271882	0.86[CHB][hapmap]
rs3803919	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes]
rs4458132	0.90[EUR][1000 genomes]
rs4808768	0.86[EUR][1000 genomes]
rs55650549	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62120367	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62120368	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62120382	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62120383	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62120385	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62120388	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62120393	0.90[EUR][1000 genomes]
rs6512247	0.87[YRI][hapmap]
rs7245576	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7246274	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs7249773	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7259695	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8100626	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs8104010	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8109807	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
5	nsv911245	chr19:18206681-18338101	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv911248	chr19:18224729-18338101	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv911249	chr19:18224729-18375846	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv911250	chr19:18224729-18376522	Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription 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 miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
11	nsv911252	chr19:18234588-18338101	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
13	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
14	nsv911254	chr19:18248146-18310678	Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv911256	chr19:18255359-18338101	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
16	nsv911260	chr19:18288069-18386798	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
17	nsv911261	chr19:18288947-18311199	Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
18	nsv911262	chr19:18288947-18312453	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
19	nsv828470	chr19:18289598-18311602	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
20	nsv828471	chr19:18293567-18311602	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
21	nsv819691	chr19:18294153-18312275	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18305200-18308200	Weak transcription	Brain Substantia Nigra	brain
2	chr19:18305200-18311000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:18305200-18314000	Weak transcription	HSMMtube	muscle
4	chr19:18305400-18312800	Weak transcription	Fetal Brain Male	brain
5	chr19:18305400-18313800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:18305400-18313800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:18305400-18314000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:18305400-18314200	Weak transcription	Small Intestine	intestine
9	chr19:18305600-18307000	Weak transcription	Fetal Lung	lung
10	chr19:18305600-18307200	Weak transcription	Brain Germinal Matrix	brain
11	chr19:18305600-18307200	Genic enhancers	Right Ventricle	heart
12	chr19:18305600-18308200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr19:18305600-18308400	Weak transcription	HepG2	liver
14	chr19:18305600-18311600	Strong transcription	Fetal Intestine Small	intestine
15	chr19:18305600-18313400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:18305600-18313400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr19:18305600-18313800	Weak transcription	Psoas Muscle	Psoas
18	chr19:18305600-18313800	Weak transcription	A549	lung
19	chr19:18305600-18313800	Weak transcription	NH-A	brain
20	chr19:18305600-18314000	Weak transcription	HSMM	muscle
21	chr19:18305800-18307200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:18305800-18308600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:18306000-18307000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr19:18306000-18307000	Weak transcription	Osteobl	bone
25	chr19:18306000-18307400	Strong transcription	NHEK	skin
26	chr19:18306000-18307600	Strong transcription	Dnd41	blood
27	chr19:18306000-18308400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr19:18306000-18308400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:18306000-18309400	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr19:18306000-18309600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:18306000-18310000	Strong transcription	NHLF	lung
32	chr19:18306000-18310400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr19:18306000-18311400	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr19:18306000-18311400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr19:18306000-18311400	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr19:18306000-18311600	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr19:18306000-18311600	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr19:18306000-18311600	Strong transcription	Ovary	ovary
39	chr19:18306000-18312000	Strong transcription	Brain Hippocampus Middle	brain
40	chr19:18306000-18313000	Strong transcription	Brain Cingulate Gyrus	brain
41	chr19:18306000-18313400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr19:18306000-18313600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:18306000-18313600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr19:18306000-18313600	Strong transcription	Fetal Stomach	stomach
45	chr19:18306000-18313600	Weak transcription	Stomach Mucosa	stomach
46	chr19:18306000-18313800	Weak transcription	HMEC	breast
47	chr19:18306200-18307000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr19:18306200-18309000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr19:18306200-18311600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr19:18306200-18311800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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