Variant report

Variant	rs28899170
Chromosome Location	chr2:234604230-234604231
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234463184..234465142-chr2:234603277..234605983,2	MCF-7	breast:
2	chr2:234599124..234606471-chr2:234613478..234621007,17	MCF-7	breast:
3	chr2:234473868..234476982-chr2:234602699..234604920,3	MCF-7	breast:
4	chr2:234393680..234401613-chr2:234597738..234605139,18	MCF-7	breast:
5	chr2:234597435..234606028-chr2:234613419..234620116,22	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085982	Chromatin interaction
ENSG00000224814	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10168416	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10173355	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10202865	1.00[CEU][hapmap]
rs10929302	0.81[CEU][hapmap]
rs11692664	0.82[EUR][1000 genomes]
rs11695484	0.80[CEU][hapmap]
rs17862875	0.80[CEU][hapmap]
rs17863787	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs2070959	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs2602376	0.90[CEU][hapmap]
rs2741044	0.90[CEU][hapmap]
rs2741045	0.90[CEU][hapmap]
rs2741046	0.90[CEU][hapmap]
rs4148324	0.90[CEU][hapmap]
rs4148325	0.90[CEU][hapmap]
rs6714634	0.80[CEU][hapmap]
rs6722076	0.85[CEU][hapmap]
rs6742078	0.90[CEU][hapmap]
rs6744284	0.85[CEU][hapmap]
rs7567229	0.94[EUR][1000 genomes]
rs7571915	0.82[EUR][1000 genomes]
rs887829	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234597800-234608600	Weak transcription	Gastric	stomach
2	chr2:234599400-234608000	Weak transcription	HUVEC	blood vessel
3	chr2:234600400-234608200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:234602200-234607600	Weak transcription	Pancreas	Pancrea
5	chr2:234602400-234604400	Enhancers	Hela-S3	cervix
6	chr2:234602800-234614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:234603400-234608000	Weak transcription	Stomach Mucosa	stomach
8	chr2:234603600-234604400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:234603600-234604400	Enhancers	NHEK	skin
10	chr2:234603800-234605200	Weak transcription	A549	lung
11	chr2:234603800-234607600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:234604200-234604600	Flanking Active TSS	Liver	Liver
13	chr2:234604200-234608600	Weak transcription	HepG2	liver

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