Variant report

Variant	rs12505054
Chromosome Location	chr4:55080371-55080372
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:55080360..55082057-chr4:55084802..55087150,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11133312	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133313	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133314	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12499153	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12501810	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12506783	0.92[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648347	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13139131	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17084051	0.85[AFR][1000 genomes]
rs1800809	0.85[AFR][1000 genomes]
rs1800812	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs2052697	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28436914	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28753397	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34521751	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4398585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4608869	0.84[AFR][1000 genomes]
rs4635872	0.84[AFR][1000 genomes]
rs4864842	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4864855	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864856	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864862	0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs4864863	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs60863210	0.88[AFR][1000 genomes]
rs61320297	0.90[AFR][1000 genomes]
rs6554159	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6554161	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6819779	0.81[EUR][1000 genomes]
rs6825018	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6845581	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6850748	0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs718454	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718455	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673267	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673597	0.84[AFR][1000 genomes]
rs7673625	0.90[AFR][1000 genomes]
rs7679903	0.81[AFR][1000 genomes]
rs7681399	0.82[AFR][1000 genomes]
rs7682912	0.88[JPT][hapmap]
rs7683707	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698425	0.82[AFR][1000 genomes]
rs890203	0.82[AFR][1000 genomes]
rs890206	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[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	nsv1003167	chr4:54732051-55081905	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv537096	chr4:54732051-55081905	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers 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
4	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55079000-55080400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr4:55079000-55080800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:55079000-55083600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:55079200-55080400	Enhancers	Hela-S3	cervix
5	chr4:55079400-55080600	Enhancers	NHEK	skin
6	chr4:55079400-55083600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr4:55079600-55080400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:55079600-55080400	Enhancers	Stomach Mucosa	stomach
9	chr4:55079600-55080400	Enhancers	NHDF-Ad	bronchial
10	chr4:55079600-55080600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:55079600-55080600	Enhancers	Left Ventricle	heart
12	chr4:55079800-55080400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:55079800-55080400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:55079800-55080400	Bivalent Enhancer	Fetal Intestine Small	intestine
15	chr4:55079800-55080400	Enhancers	HMEC	breast
16	chr4:55079800-55080600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:55079800-55080600	Enhancers	HUVEC	blood vessel
18	chr4:55079800-55083600	Weak transcription	Osteobl	bone
19	chr4:55079800-55083800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:55080000-55081400	Weak transcription	Small Intestine	intestine
21	chr4:55080000-55081800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr4:55080000-55083600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:55080000-55083800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:55080000-55083800	Weak transcription	Esophagus	oesophagus
25	chr4:55080000-55083800	Weak transcription	Right Ventricle	heart
26	chr4:55080200-55081800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:55080200-55083800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:55080200-55083800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:55080200-55083800	Weak transcription	Ovary	ovary
30	chr4:55080200-55083800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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