Variant report

Variant	rs11168862
Chromosome Location	chr12:49505958-49505959
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	chr12:49499760..49506124-chr12:49657415..49661017,8	K562	blood:
2	chr12:49501897..49506471-chr12:49657604..49660787,6	MCF-7	breast:
3	chr12:49497954..49506685-chr12:49522695..49526444,13	MCF-7	breast:
4	chr12:49500412..49506796-chr12:49520694..49526646,13	MCF-7	breast:
5	chr12:49481573..49488751-chr12:49501255..49506032,14	K562	blood:
6	chr12:49454631..49456849-chr12:49504734..49506537,2	K562	blood:
7	chr12:49497683..49501522-chr12:49502793..49506157,6	MCF-7	breast:
8	chr12:49493937..49507579-chr12:49519161..49528577,46	K562	blood:

No data

Variant related genes	Relation type
ENSG00000200309	Chromatin interaction
ENSG00000139549	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000139636	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1039225	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap]
rs1057548	0.80[EUR][1000 genomes]
rs10747561	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10747562	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747563	0.94[CHB][hapmap]
rs10783302	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783304	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783306	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10783307	0.88[CEU][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10783308	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875922	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10875924	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875927	0.80[EUR][1000 genomes]
rs10875928	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.87[YRI][hapmap]
rs10875931	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap]
rs10875934	0.94[CHB][hapmap]
rs11168857	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs11168867	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11168874	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168882	0.81[EUR][1000 genomes]
rs11168884	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs11168885	0.80[EUR][1000 genomes]
rs11168890	0.82[EUR][1000 genomes]
rs11168893	0.94[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap]
rs11168894	0.82[EUR][1000 genomes]
rs11168910	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap]
rs11837207	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12227296	0.82[ASN][1000 genomes]
rs12228775	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12229524	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs12306494	0.83[ASN][1000 genomes]
rs12318740	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1274726	0.83[MEX][hapmap]
rs1476137	0.92[CEU][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1476138	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1874908	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.87[YRI][hapmap]
rs1991427	0.83[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs2047101	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2114846	0.83[EUR][1000 genomes]
rs2162644	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs2241727	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279596	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2334930	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap]
rs2753	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3741621	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57853986	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7306084	0.94[CHB][hapmap]
rs73110168	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs731350	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7954521	0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs7954530	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap]
rs7957983	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7957998	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap]
rs7958241	0.87[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7958572	0.96[CEU][hapmap];0.82[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7959497	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs7969963	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7969967	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7976890	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7978448	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7978659	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9325145	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9788139	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9788140	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11168862	DDN	cis	Muscle Skeletal	GTEx
rs11168862	MCRS1	cis	cerebellum	SCAN
rs11168862	RP11-386G11.3	cis	Muscle Skeletal	GTEx
rs11168862	CCDC65	cis	Artery Aorta	GTEx
rs11168862	RHEBL1	cis	parietal	SCAN
rs11168862	POU6F1	cis	parietal	SCAN
rs11168862	TFCP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49505000-49506000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:49505000-49506200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:49505200-49506000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr12:49505200-49506000	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr12:49505200-49506400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr12:49505200-49507200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:49505200-49508000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:49505400-49508000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:49505400-49508000	Weak transcription	Osteobl	bone
10	chr12:49505400-49510800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:49505400-49510800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:49505400-49511000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:49505400-49514800	Weak transcription	HSMM	muscle
14	chr12:49505400-49521000	Weak transcription	Spleen	Spleen
15	chr12:49505600-49508000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:49505800-49506000	Enhancers	Ovary	ovary

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