Variant report

Variant	rs11979818
Chromosome Location	chr7:100293639-100293640
allele	C/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100288321..100291208-chr7:100293573..100296644,3	K562	blood:
2	chr7:100291734..100293834-chr7:100411313..100413984,2	MCF-7	breast:
3	chr7:100288992..100293891-chr7:100317292..100321001,4	MCF-7	breast:
4	chr7:100199658..100204753-chr7:100287607..100293733,10	K562	blood:
5	chr7:100292109..100293642-chr7:100462189..100464679,2	MCF-7	breast:
6	chr7:100177845..100180104-chr7:100290366..100293709,4	MCF-7	breast:
7	chr7:100287688..100293699-chr7:100300603..100306359,15	MCF-7	breast:
8	chr7:100198433..100204411-chr7:100285757..100293733,14	K562	blood:
9	chr7:100197481..100201934-chr7:100289981..100293981,6	MCF-7	breast:
10	chr7:100207033..100212293-chr7:100287661..100294075,8	MCF-7	breast:
11	chr7:100183057..100185845-chr7:100291476..100293682,3	MCF-7	breast:
12	chr7:100291258..100294008-chr7:100480725..100482428,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224729	Chromatin interaction
ENSG00000196411	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000172336	Chromatin interaction
ENSG00000106330	Chromatin interaction
ENSG00000106333	Chromatin interaction
ENSG00000130427	Chromatin interaction
ENSG00000087087	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10277087	0.89[JPT][hapmap]
rs10487157	0.85[MEX][hapmap]
rs10953300	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10953301	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10953302	0.86[ASW][hapmap]
rs11520986	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11760602	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11764045	0.85[MEX][hapmap]
rs11765509	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11769012	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11772705	1.00[ASN][1000 genomes]
rs11772849	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11973874	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11974395	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11980509	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11983334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11984421	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12531792	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532878	0.85[MEX][hapmap]
rs1734908	0.89[JPT][hapmap]
rs2075671	0.83[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs2075674	0.90[MEX][hapmap]
rs221790	0.89[JPT][hapmap]
rs221795	0.89[JPT][hapmap]
rs221801	0.89[JPT][hapmap]
rs2231172	0.84[ASW][hapmap];0.90[MEX][hapmap]
rs2272572	0.90[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2293769	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs4727459	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4729602	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4729605	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4729606	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs4729607	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs504141	0.89[JPT][hapmap]
rs507392	0.89[JPT][hapmap]
rs551238	0.89[JPT][hapmap]
rs62482249	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62482250	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62482251	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62482252	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62483567	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62483569	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62483570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942733	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[YRI][hapmap]
rs6969584	0.85[MEX][hapmap]
rs6969697	0.85[MEX][hapmap]
rs7812123	0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
3	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv888786	chr7:100159567-100313420	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv888791	chr7:100221867-100371114	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv607933	chr7:100240191-100365613	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv8184	chr7:100240737-100345945	Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv888792	chr7:100252918-100329189	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv888795	chr7:100266081-100298626	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	31 gene(s)	inside rSNPs	diseases
12	esv1804951	chr7:100275135-100374093	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11979818	PERQ1	Cis_1M	lymphoblastoid	RTeQTL
rs11979818	TSC22D4	cis	parietal	SCAN
rs11979818	MOSPD3	cis	Whole Blood	GTEx
rs11979818	PERQ1	cis	multi-tissue	Pritchard
rs11979818	DLX5	cis	cerebellum	SCAN
rs11979818	GIGYF1	cis	lymphoblastoid	seeQTL
rs11979818	MOSPD3	cis	multi-tissue	Pritchard
rs11979818	EPHB4	cis	multi-tissue	Pritchard
rs11979818	ENSG00000146830	cis	multi-tissue	Pritchard

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100290000-100293800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr7:100290600-100294000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr7:100290800-100294000	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr7:100292400-100293800	Enhancers	Primary B cells from cord blood	blood
5	chr7:100292400-100303000	Weak transcription	Right Atrium	heart
6	chr7:100292600-100293800	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr7:100292600-100294000	Enhancers	Primary B cells from peripheral blood	blood
8	chr7:100292600-100302800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:100292800-100293800	Flanking Active TSS	GM12878-XiMat	blood
10	chr7:100292800-100296600	Weak transcription	K562	blood
11	chr7:100292800-100303000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:100293000-100295800	Weak transcription	Placenta	Placenta
13	chr7:100293400-100293800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr7:100293400-100293800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr7:100293400-100294600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr7:100293400-100302800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr7:100293600-100293800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr7:100293600-100293800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
19	chr7:100293600-100293800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr7:100293600-100293800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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