Variant report

Variant	rs17152065
Chromosome Location	chr7:128073858-128073859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr7:128073504-128074024	MCF-7	breast:	n/a	chr7:128073801-128073808 chr7:128073801-128073811
2	GATA3	chr7:128073322-128074003	T-47D	breast:	n/a	chr7:128073801-128073808 chr7:128073801-128073811

No.	Distal block	Cell Line	Cell type
1	chr7:128047282..128051646-chr7:128071407..128074955,4	MCF-7	breast:
2	chr7:128066135..128077193-chr7:128094256..128102719,54	MCF-7	breast:
3	chr7:128045089..128046759-chr7:128073857..128075497,2	MCF-7	breast:
4	chr7:128071934..128079559-chr7:128081793..128086197,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228700	TF binding region
ENSG00000240758	Chromatin interaction
ENSG00000106348	Chromatin interaction
ENSG00000238590	Chromatin interaction
ENSG00000273184	Chromatin interaction
ENSG00000135245	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10228542	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10239919	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10247945	0.82[EUR][1000 genomes]
rs11562031	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12111997	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12113427	0.82[EUR][1000 genomes]
rs1560215	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28391244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28429588	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3802003	0.80[MEX][hapmap]
rs4731449	1.00[CEU][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes]
rs57075087	0.86[EUR][1000 genomes]
rs6944392	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap]
rs6978246	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72624928	0.86[EUR][1000 genomes]
rs7779455	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7779818	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7779945	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7781310	0.81[EUR][1000 genomes]
rs7783540	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7784120	1.00[CEU][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7784564	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7806193	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831124	chr7:127970345-128147910	Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	esv1801356	chr7:128073366-128084133	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17152065	CCDC136	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128051400-128086200	Weak transcription	Right Atrium	heart
2	chr7:128070200-128074800	Enhancers	Placenta	Placenta
3	chr7:128071200-128074800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr7:128071800-128074400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:128071800-128078600	Weak transcription	Adipose Nuclei	Adipose
6	chr7:128072200-128074600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:128072200-128075000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr7:128072400-128075400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr7:128072600-128074800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:128072600-128075000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr7:128072600-128075400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:128072600-128076200	Enhancers	HepG2	liver
13	chr7:128072800-128075000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr7:128072800-128075000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr7:128073000-128074000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:128073000-128075000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr7:128073000-128075000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr7:128073200-128074800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:128073400-128074000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:128073600-128074600	Flanking Active TSS	A549	lung
21	chr7:128073800-128083800	Weak transcription	Esophagus	oesophagus

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