Variant report

Variant	rs4569408
Chromosome Location	chr2:212330564-212330565
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	chr2:212328628..212332038-chr2:212332518..212335674,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10176444	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10196068	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10804195	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs10932375	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs11695594	0.84[JPT][hapmap];0.87[AMR][1000 genomes]
rs12988192	0.89[EUR][1000 genomes]
rs13025469	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13029575	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs13030346	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs13425064	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1595061	1.00[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs1595069	0.93[ASN][1000 genomes]
rs1836713	0.84[ASN][1000 genomes]
rs1836715	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs1836749	0.84[JPT][hapmap]
rs1992029	0.94[CHB][hapmap];0.94[ASN][1000 genomes]
rs2371272	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2371273	0.84[JPT][hapmap]
rs35115632	0.88[EUR][1000 genomes]
rs4100599	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs4255906	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4302167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4334429	0.95[ASN][1000 genomes]
rs4490118	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59962289	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6435628	0.80[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.96[ASN][1000 genomes]
rs6713894	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6726567	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7571402	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7577242	0.81[CEU][hapmap];0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834523	chr2:212163236-212331393	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv1000722	chr2:212272622-212465143	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv875778	chr2:212297838-212360994	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv460067	chr2:212313400-212378242	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv584317	chr2:212313400-212378242	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv2753335	chr2:212322858-212424019	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 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	chr2:212320400-212332800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:212324400-212330600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:212328600-212333800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:212328800-212332800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:212328800-212333000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:212328800-212333600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:212328800-212333800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:212329000-212333000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:212329800-212331000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr2:212329800-212331400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:212330200-212331000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:212330400-212331000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:212330400-212331200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr2:212330400-212331200	Enhancers	Cortex derived primary cultured neurospheres	brain

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