Variant report

Variant	rs12970508
Chromosome Location	chr18:13177506-13177507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:13177337..13179949-chr18:13185381..13188066,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267286	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10163609	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10164070	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11080618	0.87[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap]
rs11659979	0.81[CHB][hapmap]
rs11664469	0.87[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap]
rs11877065	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12607398	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs12957380	0.87[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap]
rs12958341	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12960349	0.87[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap]
rs12968538	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12971036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17603207	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs17604778	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17659689	0.81[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs17659896	0.87[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap]
rs2282541	0.87[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap]
rs4797729	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71353248	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7228684	0.87[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap]
rs8093576	0.81[JPT][hapmap]
rs9951766	0.83[EUR][1000 genomes];0.93[ASN][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	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv833591	chr18:13093777-13253748	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv909408	chr18:13122618-13308950	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv909409	chr18:13151544-13240284	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv909410	chr18:13151544-13308950	Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12970508	DDAH1	trans	lymphoblastoid	seeQTL
rs12970508	CEP192	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13174000-13182600	Enhancers	HepG2	liver
2	chr18:13176200-13181800	Weak transcription	Gastric	stomach
3	chr18:13176600-13177600	Flanking Active TSS	Duodenum Mucosa	Duodenum
4	chr18:13177000-13178600	Weak transcription	Small Intestine	intestine
5	chr18:13177200-13177600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr18:13177200-13178600	Weak transcription	Thymus	Thymus
7	chr18:13177200-13182600	Enhancers	Fetal Intestine Large	intestine
8	chr18:13177400-13177600	Enhancers	Primary T cells fromperipheralblood	blood
9	chr18:13177400-13177600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr18:13177400-13178200	Weak transcription	Colonic Mucosa	Colon
11	chr18:13177400-13178200	Weak transcription	Fetal Intestine Small	intestine
12	chr18:13177400-13179400	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr18:13177400-13179800	Weak transcription	Fetal Thymus	thymus
14	chr18:13177400-13181400	Enhancers	Liver	Liver

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