Variant report

Variant	rs36008241
Chromosome Location	chr11:65553306-65553307
allele	C/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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65552279..65555050-chr11:65558664..65561977,4	K562	blood:
2	chr11:65544951..65562337-chr11:65623093..65630859,34	MCF-7	breast:
3	chr11:65549748..65553562-chr11:65663861..65667886,4	K562	blood:
4	chr11:65551696..65553777-chr11:65562013..65564216,2	K562	blood:
5	chr11:65551999..65553570-chr11:65651722..65654050,2	K562	blood:
6	chr11:65338114..65341460-chr11:65551554..65554469,3	MCF-7	breast:
7	chr11:65549963..65553451-chr11:65657304..65660070,4	K562	blood:
8	chr11:65428991..65430722-chr11:65553054..65555889,2	MCF-7	breast:
9	chr11:65479523..65484500-chr11:65551483..65556601,5	MCF-7	breast:
10	chr11:65381741..65384368-chr11:65551453..65554074,4	MCF-7	breast:
11	chr11:65552272..65555849-chr11:65684886..65688039,3	MCF-7	breast:
12	chr11:65552282..65556398-chr11:65623209..65626538,5	MCF-7	breast:
13	chr11:65551697..65554555-chr11:65655334..65658299,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000172757	Chromatin interaction
ENSG00000175550	Chromatin interaction
ENSG00000197136	Chromatin interaction
ENSG00000173465	Chromatin interaction
ENSG00000173327	Chromatin interaction
ENSG00000172818	Chromatin interaction
ENSG00000175602	Chromatin interaction
ENSG00000175573	Chromatin interaction
ENSG00000176973	Chromatin interaction
ENSG00000172977	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000172732	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11600035	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603206	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12802560	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17491607	1.00[JPT][hapmap]
rs2277304	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34509162	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs491666	0.87[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs501337	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs523521	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs530405	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs553980	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs554863	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56164300	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs561924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604949	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67901563	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67995174	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71197355	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs732072	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
2	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
3	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
4	nsv897758	chr11:65490756-65564035	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv897759	chr11:65543827-65554502	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
6	nsv897760	chr11:65545306-65559266	Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv3321581	chr11:65552901-65555749	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs36008241	KCNK4	cis	cerebellum	SCAN
rs36008241	RNASEH2C	cis	parietal	SCAN
rs36008241	PRDX5	cis	parietal	SCAN
rs36008241	TCIRG1	cis	parietal	SCAN
rs36008241	PKM2	trans	parietal	SCAN
rs36008241	KAT5	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65548600-65553400	Weak transcription	Gastric	stomach
2	chr11:65549200-65554200	Weak transcription	Right Atrium	heart
3	chr11:65549600-65553400	Weak transcription	Colonic Mucosa	Colon
4	chr11:65549600-65553400	Weak transcription	Pancreas	Pancrea
5	chr11:65551200-65553400	Bivalent Enhancer	Thymus	Thymus
6	chr11:65551200-65555600	Bivalent Enhancer	Fetal Thymus	thymus
7	chr11:65551400-65553400	Enhancers	Esophagus	oesophagus
8	chr11:65552000-65553800	Weak transcription	NHEK	skin
9	chr11:65552200-65553800	Weak transcription	HMEC	breast
10	chr11:65552400-65553400	Enhancers	Duodenum Mucosa	Duodenum
11	chr11:65552600-65553400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr11:65552600-65553800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr11:65552600-65553800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
14	chr11:65552600-65554000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr11:65552800-65553400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr11:65552800-65553400	Bivalent Enhancer	HepG2	liver
17	chr11:65552800-65553600	Bivalent Enhancer	Primary T cells from cord blood	blood
18	chr11:65552800-65553600	Enhancers	Placenta Amnion	Placenta Amnion
19	chr11:65552800-65553600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
20	chr11:65552800-65553800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr11:65552800-65553800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
22	chr11:65552800-65554000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
23	chr11:65552800-65554000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr11:65552800-65554600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
25	chr11:65553000-65553600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
26	chr11:65553000-65553600	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr11:65553000-65553600	Bivalent Enhancer	Placenta	Placenta
28	chr11:65553000-65553600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
29	chr11:65553000-65553600	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr11:65553000-65553800	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr11:65553000-65554200	Bivalent Enhancer	GM12878-XiMat	blood
32	chr11:65553200-65553400	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:65553200-65553400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
34	chr11:65553200-65553400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:65553200-65553600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
36	chr11:65553200-65553600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr11:65553200-65553600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
38	chr11:65553200-65553600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr11:65553200-65553600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr11:65553200-65553600	Bivalent Enhancer	Fetal Intestine Large	intestine
41	chr11:65553200-65553600	Bivalent Enhancer	Fetal Intestine Small	intestine
42	chr11:65553200-65553800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:65553200-65553800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
44	chr11:65553200-65554200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood

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