Variant report

Variant	rs12653844
Chromosome Location	chr5:58598853-58598854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10054481	0.85[ASN][1000 genomes]
rs10077993	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10472101	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs10472102	0.94[CHB][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs11955452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11956680	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655617	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs13359998	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1374028	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28372523	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4700335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[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	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1030117	chr5:58587672-58637179	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58593000-58611200	Weak transcription	Right Ventricle	heart
2	chr5:58593200-58612600	Weak transcription	Fetal Lung	lung
3	chr5:58593200-58613400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:58593800-58604800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr5:58594000-58612800	Weak transcription	Stomach Mucosa	stomach
6	chr5:58594400-58606000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:58595400-58604600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:58595600-58609000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:58597000-58607600	Weak transcription	Psoas Muscle	Psoas
10	chr5:58597800-58604600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:58598000-58599200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:58598000-58604400	Weak transcription	Fetal Intestine Small	intestine
13	chr5:58598000-58604600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:58598000-58607800	Weak transcription	Fetal Heart	heart
15	chr5:58598000-58608600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr5:58598000-58612600	Weak transcription	Fetal Intestine Large	intestine
17	chr5:58598000-58612800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:58598000-58612800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:58598200-58602000	Weak transcription	Hela-S3	cervix
20	chr5:58598200-58604600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:58598400-58600400	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr5:58598800-58599800	Enhancers	A549	lung

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