Variant report

Variant	rs7105122
Chromosome Location	chr11:47449544-47449545
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr11:47445853-47449989	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47448979..47451743-chr11:47463608..47465807,2	K562	blood:
2	chr11:47446295..47450524-chr11:47461441..47464685,6	MCF-7	breast:
3	chr11:47449067..47450905-chr11:47458013..47460570,2	MCF-7	breast:
4	chr11:47449466..47452099-chr11:47461409..47464766,3	MCF-7	breast:
5	chr11:47398927..47401374-chr11:47448250..47449858,2	K562	blood:

No data

Variant related genes	Relation type
PSMC3	TF binding region
ENSG00000066336	Chromatin interaction
ENSG00000252327	Chromatin interaction
ENSG00000165917	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1044269	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs10742805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10742806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10742816	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs10769267	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11819955	0.93[JPT][hapmap]
rs11820650	0.84[ASN][1000 genomes]
rs11820680	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11821917	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs11824864	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs11827106	0.82[ASN][1000 genomes]
rs11828339	0.92[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12282783	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12419342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474056	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs17198158	0.92[GIH][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs17790804	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2138767	0.92[GIH][hapmap];0.94[JPT][hapmap];0.87[MKK][hapmap]
rs2242511	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs3740684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3740685	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3781628	0.83[ASN][1000 genomes]
rs3824867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3847503	0.92[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4147730	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs4237544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4282946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752783	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs4752786	0.92[GIH][hapmap];0.94[JPT][hapmap];0.87[MKK][hapmap]
rs4752829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4752836	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752839	0.84[GIH][hapmap];0.89[JPT][hapmap]
rs4752843	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs4752992	0.83[ASN][1000 genomes]
rs56756748	0.80[ASN][1000 genomes]
rs60380053	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60882887	0.82[ASN][1000 genomes]
rs61000762	0.85[ASN][1000 genomes]
rs7101772	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7104366	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7105907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7107853	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7108143	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7111873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7117277	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7119556	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7125468	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7126210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7130693	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs753812	0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7931089	0.92[JPT][hapmap]
rs7948705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9666924	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs9734013	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9919526	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers 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 miRNA target site	62 gene(s)	inside rSNPs	diseases
3	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv825871	chr11:47376020-47457537	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers 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	39 gene(s)	inside rSNPs	diseases
6	nsv554210	chr11:47380593-47449544	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
7	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
9	nsv975328	chr11:47446815-47471052	Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7105122	MDK	cis	parietal	SCAN
rs7105122	PSMC3	cis	cerebellum	SCAN
rs7105122	MADD	cis	parietal	SCAN
rs7105122	PTPRJ	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47448600-47449600	Weak transcription	HSMMtube	muscle
2	chr11:47448600-47452000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:47448600-47452200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:47448600-47459600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:47448600-47488400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:47448800-47449800	Flanking Active TSS	Hela-S3	cervix
7	chr11:47448800-47452000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:47448800-47452000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:47448800-47453000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr11:47448800-47453000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr11:47448800-47454800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr11:47449000-47451400	Weak transcription	Fetal Thymus	thymus
13	chr11:47449000-47451600	Weak transcription	Thymus	Thymus
14	chr11:47449000-47452000	Weak transcription	Primary T cells from cord blood	blood
15	chr11:47449000-47452200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:47449000-47453200	Weak transcription	Psoas Muscle	Psoas
17	chr11:47449000-47454800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr11:47449000-47454800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr11:47449000-47454800	Weak transcription	HSMM	muscle
20	chr11:47449000-47457200	Weak transcription	Right Atrium	heart
21	chr11:47449000-47459200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:47449000-47459400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr11:47449200-47449600	Weak transcription	Fetal Muscle Leg	muscle
24	chr11:47449200-47451600	Weak transcription	Liver	Liver
25	chr11:47449400-47449800	Enhancers	A549	lung
26	chr11:47449400-47449800	Flanking Active TSS	HepG2	liver

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