Variant report

Variant	rs4468326
Chromosome Location	chr11:17041034-17041035
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:17034691..17036893-chr11:17040088..17042253,2	K562	blood:
2	chr11:17040265..17042474-chr11:17045522..17047105,2	K562	blood:
3	chr11:16988453..16990354-chr11:17039773..17042138,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184669	Chromatin interaction
ENSG00000166689	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10832725	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10832727	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11024113	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11024116	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11024130	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11024131	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11024186	0.83[LWK][hapmap]
rs12288579	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12293395	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12794156	0.86[EUR][1000 genomes]
rs34902253	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4237716	0.86[JPT][hapmap]
rs4255517	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4456241	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4517490	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4757470	0.86[JPT][hapmap]
rs4757473	0.86[JPT][hapmap]
rs56030184	0.82[EUR][1000 genomes]
rs6486345	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6486346	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6486347	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6486348	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71047522	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7106954	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7130826	1.00[ASW][hapmap];0.95[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];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7924495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7929927	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7934571	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7934608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7934694	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7935162	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7935420	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7935677	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7937770	0.94[ASN][1000 genomes]
rs7937880	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7949405	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7950225	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7952426	0.92[AMR][1000 genomes];0.88[EUR][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	nsv832077	chr11:16834545-17059176	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv825771	chr11:17027229-17048360	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv467711	chr11:17027555-17320797	Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv553568	chr11:17027555-17320797	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4468326	PDE3B	cis	parietal	SCAN
rs4468326	BTBD10	cis	parietal	SCAN
rs4468326	NUCB2	Cis_1M	lymphoblastoid	RTeQTL
rs4468326	TSG101	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17037000-17042400	Weak transcription	Liver	Liver
2	chr11:17037000-17050200	Weak transcription	Adipose Nuclei	Adipose
3	chr11:17037200-17042800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:17037200-17043000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr11:17037200-17050400	Weak transcription	Brain Anterior Caudate	brain
6	chr11:17037200-17056000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr11:17037400-17044400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr11:17037600-17042600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr11:17037600-17042800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:17037600-17046400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:17037600-17048400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr11:17037600-17049400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr11:17037600-17058400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr11:17037600-17058600	Weak transcription	Gastric	stomach
15	chr11:17037800-17044600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr11:17037800-17048200	Weak transcription	Stomach Mucosa	stomach
17	chr11:17037800-17057400	Weak transcription	Fetal Stomach	stomach
18	chr11:17037800-17057800	Weak transcription	Pancreas	Pancrea
19	chr11:17038000-17042400	Weak transcription	A549	lung
20	chr11:17038000-17043000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:17038800-17046200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr11:17039600-17049600	Weak transcription	Thymus	Thymus
23	chr11:17040400-17041200	Enhancers	Fetal Intestine Large	intestine
24	chr11:17040400-17042400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr11:17040600-17041400	Enhancers	HepG2	liver
26	chr11:17041000-17041200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:17041000-17041600	Enhancers	Fetal Intestine Small	intestine
28	chr11:17041000-17041600	Enhancers	HSMM	muscle
29	chr11:17041000-17042000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links