Variant report

Variant	rs12655617
Chromosome Location	chr5:58589499-58589500
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10054481	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10077993	0.80[ASN][1000 genomes]
rs10472101	0.85[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]
rs10472102	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]
rs10491353	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11955452	0.91[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs11956680	0.86[ASN][1000 genomes]
rs12653844	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs12658554	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13359998	0.86[ASN][1000 genomes]
rs1374028	0.88[CHD][hapmap];0.81[JPT][hapmap]
rs28372523	0.80[ASN][1000 genomes]
rs4700335	0.94[CHB][hapmap];0.85[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12655617	PART1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58574200-58590200	Weak transcription	Right Atrium	heart
2	chr5:58583600-58589600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr5:58583600-58592400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:58583600-58592600	Weak transcription	Psoas Muscle	Psoas
5	chr5:58583600-58596400	Weak transcription	Esophagus	oesophagus
6	chr5:58583800-58591200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:58584000-58591800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:58584000-58596400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:58584800-58592400	Weak transcription	Fetal Intestine Large	intestine
10	chr5:58587800-58589800	Enhancers	HUVEC	blood vessel
11	chr5:58587800-58592800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:58588000-58592400	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:58588200-58591200	Weak transcription	Fetal Heart	heart
14	chr5:58588400-58590200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:58588400-58590200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:58588400-58591400	Genic enhancers	A549	lung
17	chr5:58588600-58589800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:58588600-58590000	Enhancers	HMEC	breast
19	chr5:58588600-58590600	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr5:58588600-58592400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:58588600-58592400	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr5:58588800-58592200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:58588800-58592400	Enhancers	Hela-S3	cervix
24	chr5:58589000-58592400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr5:58589000-58592400	Enhancers	Colon Smooth Muscle	Colon
26	chr5:58589200-58589600	Weak transcription	NHEK	skin
27	chr5:58589400-58589600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr5:58589400-58589800	Enhancers	Left Ventricle	heart
29	chr5:58589400-58590200	Enhancers	Stomach Mucosa	stomach
30	chr5:58589400-58591400	Enhancers	Rectal Smooth Muscle	rectum

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