Variant report

Variant	rs17128261
Chromosome Location	chr8:19211916-19211917
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10088460	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10089751	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10104268	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10503654	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11204032	0.84[CEU][hapmap];0.94[GIH][hapmap]
rs11985385	0.93[ASN][1000 genomes]
rs11991640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11995233	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12334513	0.81[JPT][hapmap]
rs13279141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13279165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13439427	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17116609	0.84[CEU][hapmap]
rs17128244	0.91[GIH][hapmap];0.82[LWK][hapmap];0.81[YRI][hapmap]
rs17128263	0.81[JPT][hapmap]
rs17128267	0.81[JPT][hapmap]
rs17128269	0.81[JPT][hapmap]
rs17128272	0.81[JPT][hapmap]
rs2410609	0.84[CEU][hapmap]
rs28525153	0.93[ASN][1000 genomes]
rs34246553	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34459390	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36023529	0.90[AFR][1000 genomes]
rs4921637	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs56124433	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6586826	0.84[CEU][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7001652	0.93[ASN][1000 genomes]
rs7015405	0.94[GIH][hapmap]
rs73599100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73599101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7829274	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026466	chr8:18433493-19271274	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv539520	chr8:18433493-19271274	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1015395	chr8:18489538-19370258	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv429907	chr8:18578720-19398220	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv890610	chr8:18749120-19260599	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv949745	chr8:18826830-19363963	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1016482	chr8:18834807-19339487	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv890614	chr8:18838764-19274793	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv533109	chr8:18845845-19456780	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv1016993	chr8:18855623-19311731	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
11	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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	18 gene(s)	inside rSNPs	diseases
12	nsv1033229	chr8:19081684-19271274	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
13	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
14	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17128261	LZTS1	cis	parietal	SCAN
rs17128261	MTMR7	cis	parietal	SCAN
rs17128261	PCM1	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19173600-19254800	Weak transcription	Colonic Mucosa	Colon
2	chr8:19174000-19223600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr8:19174200-19220400	Weak transcription	HSMM	muscle
4	chr8:19186200-19229800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr8:19194400-19215200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr8:19195600-19231200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr8:19196400-19215200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr8:19196400-19220400	Weak transcription	HMEC	breast
9	chr8:19196800-19213800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr8:19198800-19214800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr8:19202800-19213800	Weak transcription	Placenta	Placenta
12	chr8:19203000-19218200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr8:19204800-19215000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr8:19204800-19215200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr8:19205000-19214000	Weak transcription	Fetal Stomach	stomach
16	chr8:19205000-19214800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr8:19205000-19215000	Weak transcription	Gastric	stomach
18	chr8:19205000-19215200	Weak transcription	Right Atrium	heart
19	chr8:19205600-19214800	Weak transcription	NHLF	lung
20	chr8:19205600-19215200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr8:19205600-19220600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr8:19205600-19221000	Weak transcription	Stomach Mucosa	stomach
23	chr8:19205800-19215000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr8:19205800-19215000	Weak transcription	Pancreas	Pancrea
25	chr8:19205800-19215200	Weak transcription	NHEK	skin
26	chr8:19205800-19219000	Weak transcription	Adipose Nuclei	Adipose
27	chr8:19205800-19220800	Weak transcription	Lung	lung
28	chr8:19205800-19221000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr8:19206000-19212400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr8:19206000-19212400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr8:19206600-19214400	Weak transcription	Fetal Intestine Large	intestine
32	chr8:19206600-19223800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr8:19208400-19213400	Weak transcription	Fetal Intestine Small	intestine
34	chr8:19208400-19213600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr8:19208400-19214200	Weak transcription	HepG2	liver
36	chr8:19208400-19214400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr8:19208400-19214600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr8:19208400-19214800	Weak transcription	Osteobl	bone
39	chr8:19208400-19215200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr8:19208400-19216000	Weak transcription	Esophagus	oesophagus
41	chr8:19208400-19221200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr8:19208400-19231200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr8:19208600-19214800	Weak transcription	Liver	Liver
44	chr8:19208800-19215400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr8:19209800-19212400	Strong transcription	Hela-S3	cervix
46	chr8:19210200-19214800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr8:19210400-19213000	Weak transcription	Fetal Brain Male	brain
48	chr8:19210600-19212200	Weak transcription	Fetal Kidney	kidney
49	chr8:19210600-19216800	Weak transcription	Small Intestine	intestine
50	chr8:19211400-19224600	Strong transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links