Variant report

Variant	rs6696556
Chromosome Location	chr1:152430842-152430843
allele	G/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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:152161771..152162690-chr1:152430545..152431431,5	MCF-7	breast:
2	chr1:152413327..152415883-chr1:152427595..152432391,4	MCF-7	breast:
3	chr1:152427149..152431116-chr1:152432687..152434302,3	MCF-7	breast:
4	chr1:152413332..152413978-chr1:152430103..152431369,3	MCF-7	breast:
5	chr1:152411861..152413555-chr1:152429926..152432618,2	MCF-7	breast:
6	chr1:152370854..152372408-chr1:152430534..152432083,18	MCF-7	breast:
7	chr1:152370872..152372629-chr1:152430126..152431524,8	MCF-7	breast:
8	chr1:152160345..152163243-chr1:152429950..152431845,23	MCF-7	breast:
9	chr1:152160802..152161752-chr1:152430569..152431282,4	MCF-7	breast:
10	chr1:152369802..152370305-chr1:152430586..152431135,2	K562	blood:
11	chr1:152024732..152025426-chr1:152430646..152431152,2	MCF-7	breast:
12	chr1:152025140..152025697-chr1:152430572..152431473,3	K562	blood:
13	chr1:152162008..152163068-chr1:152430225..152431533,6	K562	blood:
14	chr1:152160826..152162605-chr1:152429610..152431734,2	MCF-7	breast:
15	chr1:152430033..152432133-chr20:52323430..52325035,2	MCF-7	breast:
16	chr1:152163573..152164481-chr1:152430706..152431340,2	MCF-7	breast:
17	chr1:152319690..152320209-chr1:152430662..152431472,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000183586	Chromatin interaction
ENSG00000237975	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10888486	0.83[CEU][hapmap]
rs11577946	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11579266	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12029431	0.83[CEU][hapmap]
rs12049036	0.83[CEU][hapmap]
rs12067942	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16834090	0.81[GIH][hapmap]
rs1923493	0.83[CEU][hapmap]
rs1923501	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2146117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36061814	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3753443	0.83[CEU][hapmap]
rs3753444	0.83[CEU][hapmap]
rs3829868	0.83[CEU][hapmap]
rs4285700	0.83[CEU][hapmap]
rs4845771	0.86[CHD][hapmap];0.81[GIH][hapmap]
rs499997	0.80[AFR][1000 genomes]
rs556124	0.80[AFR][1000 genomes]
rs56325026	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72698953	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72698960	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72698963	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72698964	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72698999	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7521839	0.83[CEU][hapmap]

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	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv872443	chr1:152400055-152459747	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv872444	chr1:152400361-152440753	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv824664	chr1:152409024-152434443	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv463850	chr1:152411090-152434009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv547858	chr1:152411090-152434009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv872445	chr1:152411813-152440753	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6696556	GABPB2	cis	cerebellum	SCAN
rs6696556	AQP10	cis	parietal	SCAN
rs6696556	IVL	cis	parietal	SCAN
rs6696556	CRNN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152430000-152432400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:152430000-152432400	Weak transcription	Brain Substantia Nigra	brain
3	chr1:152430200-152432200	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:152430600-152431000	Enhancers	Brain Anterior Caudate	brain
5	chr1:152430800-152431000	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr1:152430800-152431000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr1:152430800-152431200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr1:152430800-152431200	Bivalent Enhancer	Fetal Kidney	kidney
9	chr1:152430800-152431400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:152430800-152431400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr1:152430800-152431400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:152430800-152431400	Enhancers	Liver	Liver
13	chr1:152430800-152431400	Enhancers	Colon Smooth Muscle	Colon
14	chr1:152430800-152431600	Enhancers	Primary T cells fromperipheralblood	blood
15	chr1:152430800-152431600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:152430800-152431600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr1:152430800-152431600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:152430800-152432400	Enhancers	Primary B cells from peripheral blood	blood

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