Variant report

Variant	rs11725662
Chromosome Location	chr4:121671965-121671966
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs13110308	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13116962	1.00[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13124620	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1355439	0.84[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1397766	0.82[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1588523	0.86[LWK][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap]
rs2136998	1.00[ASW][hapmap];0.85[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2292395	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2390053	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs3789140	0.94[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6534215	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6823191	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6825664	0.86[ASN][1000 genomes]
rs6827372	0.84[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6845666	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6851591	0.84[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7675540	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv879852	chr4:121108734-121768496	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1004485	chr4:121542992-121716769	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv916737	chr4:121589793-121748847	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv461634	chr4:121623057-121765527	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv595334	chr4:121623057-121765527	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1013704	chr4:121657648-121791601	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121652000-121673600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr4:121652600-121687000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:121653200-121672200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr4:121662400-121673200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:121663000-121672000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:121668400-121690400	Weak transcription	Osteobl	bone
7	chr4:121668600-121673600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
8	chr4:121669200-121672200	Strong transcription	Fetal Muscle Trunk	muscle
9	chr4:121669400-121672800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:121670000-121675000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:121670400-121672400	ZNF genes & repeats	Lung	lung
12	chr4:121670400-121673000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:121670400-121673000	ZNF genes & repeats	Fetal Muscle Leg	muscle
14	chr4:121670600-121672400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:121670600-121672400	ZNF genes & repeats	Aorta	Aorta
16	chr4:121670600-121672400	ZNF genes & repeats	Fetal Stomach	stomach
17	chr4:121670600-121673000	Strong transcription	Stomach Smooth Muscle	stomach
18	chr4:121670600-121673800	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:121670800-121672000	Strong transcription	Right Ventricle	heart
20	chr4:121671000-121672000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
21	chr4:121671000-121673000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:121671000-121675000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr4:121671200-121672400	ZNF genes & repeats	Fetal Intestine Small	intestine
24	chr4:121671400-121672000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
25	chr4:121671400-121673200	ZNF genes & repeats	Fetal Lung	lung
26	chr4:121671600-121672200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:121671600-121672400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:121671600-121672400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:121671600-121672400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:121671600-121672400	ZNF genes & repeats	Fetal Intestine Large	intestine
31	chr4:121671800-121672000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:121671800-121672000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:121671800-121684200	Weak transcription	Ovary	ovary
34	chr4:121671800-121697000	Weak transcription	Pancreas	Pancrea
35	chr4:121671800-121728600	Weak transcription	Left Ventricle	heart

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