Variant report

Variant	rs7661259
Chromosome Location	chr4:55897310-55897311
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10018070	0.86[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13101523	0.95[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13111963	0.81[ASN][1000 genomes]
rs13112551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13142103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13144674	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13144875	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28744674	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34227858	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4259119	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4333248	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4457012	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4566712	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4571397	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4577640	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4582210	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4596303	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap]
rs4864529	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864530	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5018667	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57528857	0.95[ASN][1000 genomes]
rs6554225	0.83[ASN][1000 genomes]
rs6554226	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6554228	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554229	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66459610	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66506770	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6816847	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6820336	0.96[ASN][1000 genomes]
rs6820371	0.96[ASN][1000 genomes]
rs6844468	0.95[ASN][1000 genomes]
rs6845385	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7658751	0.83[ASN][1000 genomes]
rs7677709	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7679094	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv829939	chr4:55856771-56005011	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv432603	chr4:55877236-55970782	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv524342	chr4:55891531-55921535	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55892200-55897400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:55894200-55898600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:55895600-55897600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:55895800-55897600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr4:55895800-55904600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr4:55896000-55897400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:55896400-55898600	Weak transcription	Right Atrium	heart
8	chr4:55896400-55898800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr4:55896400-55904400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:55896600-55898800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:55896600-55898800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:55896800-55897800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:55896800-55905000	Enhancers	HMEC	breast
14	chr4:55897000-55897600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr4:55897200-55898200	Enhancers	Duodenum Mucosa	Duodenum
16	chr4:55897200-55898800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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