Variant report

Variant	rs12200888
Chromosome Location	chr6:119992869-119992870
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:119984260..119986895-chr6:119991023..119994308,3	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10484866	0.87[EUR][1000 genomes]
rs11153843	0.87[EUR][1000 genomes]
rs11757432	0.87[EUR][1000 genomes]
rs11757501	0.96[EUR][1000 genomes]
rs11757553	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12198857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204573	0.89[CEU][hapmap]
rs12204589	0.81[EUR][1000 genomes]
rs12207073	0.87[EUR][1000 genomes]
rs12211120	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12211253	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12211678	0.86[EUR][1000 genomes]
rs12212825	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13193709	0.87[EUR][1000 genomes]
rs13194523	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13208384	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1341497	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1417843	0.89[EUR][1000 genomes]
rs17081512	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17174818	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17175669	0.96[EUR][1000 genomes]
rs17254459	0.89[EUR][1000 genomes]
rs2077847	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34024607	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34663676	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57243130	0.81[EUR][1000 genomes]
rs6914520	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6922820	0.96[EUR][1000 genomes]
rs727606	0.96[EUR][1000 genomes]
rs731487	0.86[ASW][hapmap];0.89[CEU][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs7757952	0.82[EUR][1000 genomes]
rs7764925	0.96[EUR][1000 genomes]
rs9285434	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9320701	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9481956	0.87[EUR][1000 genomes]
rs9489780	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9489782	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs991356	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1027904	chr6:119709488-120001986	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv533518	chr6:119712186-119998618	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3442553	chr6:119742069-120076777	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1027370	chr6:119869409-120056608	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538431	chr6:119869409-120056608	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119991800-119994000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr6:119991800-119995000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:119991800-120008000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:119992000-119993000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr6:119992200-119993000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr6:119992200-119994200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr6:119992200-119995000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr6:119992200-119995200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr6:119992400-119993400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:119992600-119993800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:119992800-119993800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:119992800-119993800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:119992800-119993800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:119992800-120009600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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