Variant report

Variant	rs17222290
Chromosome Location	chr12:47548864-47548865
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:47544469..47546961-chr12:47548595..47550725,2	MCF-7	breast:
2	chr12:47547612..47549821-chr12:47551501..47553905,2	K562	blood:
3	chr12:47533951..47536352-chr12:47547162..47551314,3	K562	blood:
4	chr12:47540570..47543353-chr12:47547169..47548960,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10881045	0.81[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs10881047	0.90[AMR][1000 genomes]
rs11183738	0.81[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes]
rs11183740	0.91[AMR][1000 genomes]
rs11183741	0.91[AMR][1000 genomes]
rs11183744	0.91[AMR][1000 genomes]
rs11183751	0.94[AMR][1000 genomes]
rs11183752	0.81[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes]
rs11183759	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11183760	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11183761	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11183776	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11183777	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11183779	0.85[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs11183783	0.84[CEU][hapmap]
rs12368600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370192	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12370851	0.90[AMR][1000 genomes]
rs17821774	0.84[ASW][hapmap]
rs1917655	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1917656	0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1917657	1.00[ASW][hapmap];0.81[CEU][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes]
rs2408718	0.84[ASW][hapmap]
rs35456925	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73101453	0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73108103	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73108123	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs732523	0.84[ASW][hapmap]
rs7974410	0.84[ASW][hapmap]
rs832729	0.89[CEU][hapmap]
rs952967	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[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	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2751100	chr12:47541390-47746157	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17222290	HDAC7	cis	parietal	SCAN
rs17222290	DNAJC22	cis	cerebellum	SCAN
rs17222290	DHH	cis	cerebellum	SCAN
rs17222290	CCDC65	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47535800-47549600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:47535800-47554600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:47536000-47549600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:47536000-47550000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:47536000-47550200	Weak transcription	Adipose Nuclei	Adipose
6	chr12:47536000-47550200	Weak transcription	Aorta	Aorta
7	chr12:47536000-47578000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:47536200-47564200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:47536400-47549400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr12:47539400-47550000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:47540000-47549200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr12:47540000-47549200	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:47541600-47558400	Weak transcription	NHEK	skin
14	chr12:47541800-47549200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:47544600-47549400	Weak transcription	Lung	lung
16	chr12:47545800-47549000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr12:47545800-47549200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:47547600-47549200	Enhancers	A549	lung
19	chr12:47547800-47550600	Enhancers	Ovary	ovary
20	chr12:47548000-47549000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:47548000-47549200	Weak transcription	K562	blood
22	chr12:47548000-47549400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr12:47548400-47551400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr12:47548600-47549400	Weak transcription	Pancreas	Pancrea
25	chr12:47548600-47550800	Enhancers	Colon Smooth Muscle	Colon
26	chr12:47548800-47552400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links