Variant report

Variant	rs9304098
Chromosome Location	chr18:29083630-29083631
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:29080297..29083464-chr18:29083547..29086345,4	K562	blood:
2	chr18:29076737..29079716-chr18:29083540..29087403,5	K562	blood:
3	chr18:29077157..29080262-chr18:29081706..29084884,3	K562	blood:
4	chr18:29082210..29085319-chr18:29089707..29093199,4	K562	blood:
5	chr18:29079215..29080950-chr18:29081744..29084257,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266521	Chromatin interaction
ENSG00000046604	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1031729	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs11081701	0.81[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1350731	0.85[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1460602	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs17660585	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1824477	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1841396	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2212617	0.82[ASN][1000 genomes]
rs2212618	0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2219584	0.85[CEU][hapmap];0.84[CHB][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2704050	0.89[CEU][hapmap];0.85[CHB][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2704051	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2704052	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2704053	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2704055	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2848677	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2848680	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2848681	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4799310	0.93[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4799573	0.87[ASN][1000 genomes]
rs6506927	0.82[CHB][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6506928	0.85[CEU][hapmap];0.84[CHB][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7227343	0.81[CHD][hapmap];0.80[ASN][1000 genomes]
rs7227984	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7231288	0.85[ASN][1000 genomes]
rs7231553	0.85[ASN][1000 genomes]
rs7232282	0.87[ASN][1000 genomes]
rs7235272	0.85[ASN][1000 genomes]
rs7236324	0.87[ASN][1000 genomes]
rs7236469	0.85[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7238729	0.87[ASN][1000 genomes]
rs7240824	0.94[ASN][1000 genomes]
rs7241107	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73414280	0.86[ASN][1000 genomes]
rs73953901	0.87[ASN][1000 genomes]
rs8093731	0.81[YRI][hapmap]
rs9304097	0.86[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9304099	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9941421	0.85[CEU][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9945031	0.96[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9945420	0.98[ASN][1000 genomes]
rs9951843	0.83[ASN][1000 genomes]
rs9961910	0.83[ASN][1000 genomes]
rs9961920	0.87[ASN][1000 genomes]
rs9961925	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9962121	0.84[CHB][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs9962318	0.87[ASN][1000 genomes]
rs9962333	0.98[ASN][1000 genomes]
rs9962423	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066692	chr18:28856066-29190505	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543674	chr18:28856066-29190505	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv916545	chr18:28898800-29166364	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer 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 miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833615	chr18:29008396-29192976	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9304098	DSC1	cis	parietal	SCAN
rs9304098	GPX3	trans	brain	seeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29080400-29085800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr18:29080400-29091000	Weak transcription	Colonic Mucosa	Colon
3	chr18:29080600-29084000	Weak transcription	K562	blood
4	chr18:29080600-29084400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr18:29080600-29084600	Weak transcription	Right Atrium	heart
6	chr18:29080600-29084600	Weak transcription	Right Ventricle	heart
7	chr18:29080600-29088400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr18:29080600-29088600	Weak transcription	HMEC	breast
9	chr18:29080600-29088800	Weak transcription	A549	lung
10	chr18:29080600-29089600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr18:29080600-29093200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr18:29080600-29100000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr18:29080600-29100400	Weak transcription	Fetal Thymus	thymus
14	chr18:29080800-29084200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr18:29080800-29084200	Weak transcription	Fetal Heart	heart
16	chr18:29080800-29084400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr18:29080800-29084600	Weak transcription	Fetal Intestine Large	intestine
18	chr18:29080800-29084600	Weak transcription	Gastric	stomach
19	chr18:29080800-29088600	Weak transcription	Hela-S3	cervix
20	chr18:29080800-29092400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr18:29081000-29091400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr18:29081600-29084600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr18:29081600-29084600	Weak transcription	Stomach Mucosa	stomach
24	chr18:29081600-29092000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr18:29081600-29092200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr18:29081600-29092200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr18:29081600-29093200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr18:29081800-29084000	Weak transcription	Pancreas	Pancrea
29	chr18:29081800-29084400	Weak transcription	Fetal Intestine Small	intestine
30	chr18:29081800-29084400	Weak transcription	NHEK	skin
31	chr18:29081800-29088000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr18:29081800-29088600	Weak transcription	HepG2	liver
33	chr18:29081800-29092200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr18:29082800-29085200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr18:29083000-29084000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr18:29083200-29084600	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr18:29083400-29086800	Enhancers	Placenta Amnion	Placenta Amnion
38	chr18:29083400-29092600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr18:29083600-29084400	Enhancers	GM12878-XiMat	blood
40	chr18:29083600-29084600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr18:29083600-29085200	Enhancers	Sigmoid Colon	Sigmoid Colon

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