Variant report

Variant	rs12509168
Chromosome Location	chr4:78113634-78113635
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:45918563..45921114-chr4:78111513..78114166,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10009384	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10010290	0.82[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap]
rs10018359	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10025838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10026129	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10030727	0.94[ASN][1000 genomes]
rs10030735	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10030867	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs10030957	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs1006042	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10856957	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs11097704	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs11097730	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11731592	0.95[EUR][1000 genomes]
rs12508219	0.81[JPT][hapmap]
rs12640093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1477314	0.91[JPT][hapmap]
rs1559119	0.91[JPT][hapmap]
rs1559122	0.90[JPT][hapmap]
rs2042228	0.91[JPT][hapmap]
rs4241604	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs4280759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4365751	0.91[EUR][1000 genomes]
rs4518274	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs4547817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4558892	0.90[EUR][1000 genomes]
rs4563522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4576030	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4582179	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap]
rs4582180	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4859473	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs4859475	0.86[JPT][hapmap]
rs4859477	0.91[JPT][hapmap]
rs4859753	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4859754	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4859755	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4859756	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6532867	0.95[EUR][1000 genomes]
rs6532868	0.95[EUR][1000 genomes]
rs6532870	0.96[EUR][1000 genomes]
rs6532871	0.96[EUR][1000 genomes]
rs6822794	0.91[JPT][hapmap]
rs6840915	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6845599	0.96[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6845942	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6846698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6849124	0.80[CEU][hapmap]
rs6849534	0.80[CEU][hapmap]
rs6857792	0.96[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7690427	0.86[JPT][hapmap]

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	nsv879500	chr4:78045960-78115334	Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1000730	chr4:78109138-78210296	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78094400-78114200	Weak transcription	Primary B cells from cord blood	blood
2	chr4:78109000-78113800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr4:78109000-78114000	Weak transcription	Thymus	Thymus
4	chr4:78109000-78114200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr4:78109000-78114200	Weak transcription	Fetal Thymus	thymus
6	chr4:78109000-78114400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr4:78110400-78114200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr4:78110400-78114200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:78112000-78114200	Weak transcription	Placenta	Placenta
10	chr4:78112000-78114800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:78112000-78116200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:78112000-78117400	Weak transcription	Fetal Muscle Leg	muscle
13	chr4:78112000-78120600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr4:78112200-78120600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:78113400-78113800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:78113600-78118600	Weak transcription	NHEK	skin
17	chr4:78113600-78120400	Weak transcription	HMEC	breast

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