Variant report

Variant	rs7924495
Chromosome Location	chr11:17038728-17038729
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:17037168..17039319-chr11:17083342..17085313,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10832725	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10832727	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11024113	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11024116	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11024130	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11024131	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12277622	1.00[YRI][hapmap]
rs12283197	1.00[YRI][hapmap]
rs12288105	1.00[YRI][hapmap]
rs12288579	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12291395	1.00[YRI][hapmap]
rs12292965	1.00[YRI][hapmap]
rs12293395	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12293793	1.00[YRI][hapmap]
rs12794156	0.85[EUR][1000 genomes]
rs34902253	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4237716	0.86[JPT][hapmap]
rs4255517	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4456241	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4468326	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]
rs4517490	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4757470	0.86[JPT][hapmap]
rs4757473	0.86[JPT][hapmap]
rs56030184	0.81[EUR][1000 genomes]
rs6486345	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486346	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6486347	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6486348	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71047522	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7106954	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7130826	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7929927	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7934571	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7934608	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7934694	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7935162	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7935420	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7935677	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7937770	0.95[ASN][1000 genomes]
rs7937880	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7949405	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7950225	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7952426	0.85[AMR][1000 genomes];0.87[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7924495	TSG101	cis	cerebellum	SCAN
rs7924495	BTBD10	cis	parietal	SCAN
rs7924495	PDE3B	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17036600-17041000	Weak transcription	HSMMtube	muscle
2	chr11:17036800-17041000	Weak transcription	HSMM	muscle
3	chr11:17037000-17042400	Weak transcription	Liver	Liver
4	chr11:17037000-17050200	Weak transcription	Adipose Nuclei	Adipose
5	chr11:17037200-17042800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:17037200-17043000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr11:17037200-17050400	Weak transcription	Brain Anterior Caudate	brain
8	chr11:17037200-17056000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr11:17037400-17044400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr11:17037600-17040400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:17037600-17042600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr11:17037600-17042800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:17037600-17046400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:17037600-17048400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr11:17037600-17049400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr11:17037600-17058400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr11:17037600-17058600	Weak transcription	Gastric	stomach
18	chr11:17037800-17040400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr11:17037800-17040400	Weak transcription	Fetal Intestine Large	intestine
20	chr11:17037800-17040400	Weak transcription	Fetal Intestine Small	intestine
21	chr11:17037800-17040600	Weak transcription	HepG2	liver
22	chr11:17037800-17044600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr11:17037800-17048200	Weak transcription	Stomach Mucosa	stomach
24	chr11:17037800-17057400	Weak transcription	Fetal Stomach	stomach
25	chr11:17037800-17057800	Weak transcription	Pancreas	Pancrea
26	chr11:17038000-17042400	Weak transcription	A549	lung
27	chr11:17038000-17043000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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