Variant report

Variant	rs17014375
Chromosome Location	chr1:209543560-209543561
allele	G/T
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	POLR2A	chr1:209543560-209544391	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:209543378-209543604	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:209532175..209545038-chr1:209598052..209610156,35	MCF-7	breast:
2	chr1:209542346..209543898-chr1:209584985..209586763,2	MCF-7	breast:
3	chr1:209535501..209537810-chr1:209541839..209543791,2	K562	blood:
4	chr1:209527253..209544360-chr1:209599669..209610889,45	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231648	TF binding region
ENSG00000230937	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1006316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1006317	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10494921	0.85[EUR][1000 genomes]
rs11811038	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12135550	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1354850	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1354852	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1354853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1395753	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1507331	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1507335	0.89[YRI][hapmap]
rs1507336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17014320	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17014323	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17014337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17014370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17014395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17014396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1857967	0.92[CHB][hapmap]
rs4844473	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4844807	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4844809	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4844815	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4844820	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4844821	0.95[ASN][1000 genomes]
rs55684110	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58017268	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60460414	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60534728	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674793	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6681466	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74155473	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7516757	0.83[ASN][1000 genomes]
rs7516864	0.92[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7548184	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832492	chr1:209383771-209589312	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209526400-209545600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:209529800-209547000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:209535400-209543800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:209535800-209550800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:209536000-209545200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:209536000-209545600	Enhancers	HMEC	breast
7	chr1:209536800-209548600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:209537600-209548600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:209538000-209547200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:209539800-209545600	Enhancers	Fetal Brain Male	brain
11	chr1:209540200-209544600	Enhancers	Fetal Brain Female	brain
12	chr1:209540400-209549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:209540600-209546200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:209541200-209548600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:209542400-209547000	Weak transcription	Esophagus	oesophagus
16	chr1:209542400-209548800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:209542600-209543600	Weak transcription	Fetal Lung	lung
18	chr1:209542600-209548000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:209542600-209549200	Weak transcription	A549	lung
20	chr1:209543000-209543600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr1:209543000-209546800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:209543200-209544000	Enhancers	Fetal Thymus	thymus
23	chr1:209543200-209548400	Weak transcription	NHLF	lung
24	chr1:209543200-209548600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:209543200-209548800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:209543400-209544000	Flanking Active TSS	NHEK	skin
27	chr1:209543400-209548400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:209543400-209548400	Weak transcription	Hela-S3	cervix
29	chr1:209543400-209548400	Weak transcription	Osteobl	bone

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