Variant report

Variant	rs1169721
Chromosome Location	chr12:121641509-121641510
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:121639319..121642998-chr12:121646427..121652052,9	MCF-7	breast:
2	chr12:121638895..121643738-chr12:121644037..121648634,7	K562	blood:
3	chr12:121633584..121637006-chr12:121640952..121642705,3	K562	blood:
4	chr12:121613491..121614418-chr12:121640538..121641644,9	MCF-7	breast:
5	chr12:121627659..121629279-chr12:121641297..121643728,2	K562	blood:
6	chr12:121638895..121644396-chr12:121646510..121649736,6	K562	blood:
7	chr12:121638580..121643612-chr12:121646421..121651534,9	MCF-7	breast:
8	chr12:121634221..121637382-chr12:121639150..121642465,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000135124	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11065481	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1169722	0.80[CEU][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes]
rs1653586	0.88[CHB][hapmap];0.90[CHD][hapmap]
rs1653587	0.88[CHB][hapmap];0.90[CHD][hapmap]
rs1653588	0.88[CHB][hapmap]
rs1653589	0.88[CHB][hapmap];0.90[CHD][hapmap]
rs1653590	0.88[CHB][hapmap];0.90[CHD][hapmap]
rs1653593	0.88[CHB][hapmap]
rs2071272	0.88[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap]
rs2071273	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs2272076	0.88[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs2288691	0.81[ASN][1000 genomes]
rs2288693	0.88[CHB][hapmap]
rs25642	0.81[ASN][1000 genomes]
rs2567982	0.88[CHB][hapmap];0.90[CHD][hapmap]
rs2668246	0.88[CHB][hapmap]
rs3763975	0.83[ASN][1000 genomes]
rs57419819	0.88[ASN][1000 genomes]
rs57983015	0.81[ASN][1000 genomes]
rs59037892	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription 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	22 gene(s)	inside rSNPs	diseases
7	nsv899564	chr12:121641509-121689798	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv899565	chr12:121641509-121698785	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1169721	CCDC64	cis	parietal	SCAN
rs1169721	P2RX4	cis	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121624200-121647200	Weak transcription	Brain Anterior Caudate	brain
2	chr12:121625600-121647200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:121628000-121647200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:121630400-121647200	Weak transcription	Brain Hippocampus Middle	brain
5	chr12:121637200-121642800	Weak transcription	HUVEC	blood vessel
6	chr12:121639600-121641600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:121640400-121641600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:121640400-121641600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr12:121641000-121641600	Enhancers	K562	blood
10	chr12:121641000-121647000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:121641400-121642600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:121641400-121642600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:121641400-121642600	Weak transcription	Fetal Heart	heart
14	chr12:121641400-121644600	Weak transcription	Placenta	Placenta
15	chr12:121641400-121646800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:121641400-121647800	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links