Variant report

Variant	rs10497528
Chromosome Location	chr2:179825261-179825262
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179825079..179826748-chr2:179827040..179829506,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10171173	0.81[CEU][hapmap];0.91[GIH][hapmap]
rs10930845	0.80[EUR][1000 genomes]
rs10930847	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11694943	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13403584	0.81[EUR][1000 genomes]
rs16866583	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1847420	0.81[EUR][1000 genomes]
rs2200826	0.84[EUR][1000 genomes]
rs4894072	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6715920	0.81[EUR][1000 genomes]
rs6727743	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6747725	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7574599	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs924800	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv875455	chr2:179732845-179909467	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv583756	chr2:179758007-179843612	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1000545	chr2:179768359-179843612	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv875456	chr2:179775893-179896787	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv875457	chr2:179775893-179966804	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv875458	chr2:179780624-179966804	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1011538	chr2:179803786-179862194	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10497528	TTN	cis	parietal	SCAN
rs10497528	HOXD12	cis	cerebellum	SCAN
rs10497528	CCDC141	cis	parietal	SCAN
rs10497528	CCDC141	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179770000-179848200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr2:179775600-179826400	Weak transcription	Pancreas	Pancrea
3	chr2:179802800-179829400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr2:179803600-179827600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr2:179804000-179831600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:179806800-179843600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:179812600-179839000	Weak transcription	HSMMtube	muscle
8	chr2:179814000-179828200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:179816600-179841200	Weak transcription	Right Ventricle	heart
10	chr2:179819800-179825800	Weak transcription	Fetal Heart	heart
11	chr2:179821000-179828200	Strong transcription	Primary T cells from cord blood	blood
12	chr2:179823000-179826400	Weak transcription	Thymus	Thymus
13	chr2:179823800-179826200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:179824200-179825400	Strong transcription	Primary B cells from peripheral blood	blood
15	chr2:179824200-179825400	Strong transcription	Left Ventricle	heart
16	chr2:179824200-179826000	Strong transcription	Primary B cells from cord blood	blood
17	chr2:179824200-179826200	Strong transcription	Fetal Muscle Leg	muscle
18	chr2:179824200-179826800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:179824400-179828600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:179824400-179829000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:179824600-179829000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:179825200-179828400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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