Variant report

Variant	rs12188621
Chromosome Location	chr5:60595439-60595440
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:60586340..60593423-chr5:60595007..60600646,11	MCF-7	breast:
2	chr5:60590649..60593128-chr5:60594845..60596652,2	MCF-7	breast:
3	chr5:60595162..60604481-chr5:60621758..60631019,20	MCF-7	breast:
4	chr5:60593618..60596553-chr5:60596973..60598822,2	K562	blood:
5	chr5:60595107..60599156-chr5:60625279..60628331,4	K562	blood:

Variant related genes	Relation type
ENSG00000130449	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10044518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10044575	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12188882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs159373	1.00[JPT][hapmap]
rs28685817	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295523	1.00[JPT][hapmap]
rs295525	1.00[JPT][hapmap]
rs295526	1.00[JPT][hapmap]
rs295529	1.00[JPT][hapmap]
rs295530	1.00[JPT][hapmap]
rs295568	1.00[JPT][hapmap]
rs295580	1.00[JPT][hapmap]
rs298624	1.00[JPT][hapmap]
rs298626	1.00[JPT][hapmap]
rs298627	1.00[JPT][hapmap]
rs298628	1.00[JPT][hapmap]
rs298630	1.00[JPT][hapmap]
rs298631	1.00[JPT][hapmap]
rs4256302	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4382119	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4452517	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498497	1.00[JPT][hapmap]
rs557092	1.00[JPT][hapmap]
rs59628996	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603018	1.00[JPT][hapmap]
rs73105361	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73105363	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv823089	chr5:60589501-60669903	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60587000-60597400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:60587200-60597200	Weak transcription	Brain Hippocampus Middle	brain
3	chr5:60587200-60597400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:60589200-60597200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:60589400-60597000	Weak transcription	Fetal Intestine Large	intestine
6	chr5:60589400-60597400	Weak transcription	Brain Anterior Caudate	brain
7	chr5:60591800-60597400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:60593400-60595600	Enhancers	HUVEC	blood vessel
9	chr5:60593800-60597200	Enhancers	A549	lung
10	chr5:60594000-60595600	Enhancers	Pancreas	Pancrea
11	chr5:60594000-60596400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:60594000-60596400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:60594000-60596800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:60594000-60602400	Enhancers	NHDF-Ad	bronchial
15	chr5:60594000-60602800	Enhancers	HMEC	breast
16	chr5:60594200-60597000	Enhancers	NHLF	lung
17	chr5:60594200-60597400	Enhancers	Fetal Lung	lung
18	chr5:60594400-60596600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:60594400-60597000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:60594400-60599200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr5:60594600-60595800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr5:60594600-60597200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr5:60594600-60597200	Enhancers	Stomach Smooth Muscle	stomach
24	chr5:60594800-60595800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:60594800-60597000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr5:60594800-60597400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr5:60594800-60597600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr5:60595000-60595600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:60595000-60595800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:60595000-60596400	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr5:60595000-60597600	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr5:60595000-60599600	Weak transcription	Fetal Thymus	thymus
33	chr5:60595200-60595600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:60595200-60595600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:60595200-60595600	Enhancers	HSMM	muscle
36	chr5:60595200-60596000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr5:60595200-60597200	Weak transcription	Brain Substantia Nigra	brain
38	chr5:60595200-60597200	Weak transcription	Esophagus	oesophagus
39	chr5:60595200-60597200	Weak transcription	Left Ventricle	heart
40	chr5:60595200-60597200	Weak transcription	Right Atrium	heart
41	chr5:60595200-60597400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:60595200-60597400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr5:60595200-60597400	Weak transcription	Lung	lung
44	chr5:60595200-60597400	Weak transcription	Psoas Muscle	Psoas
45	chr5:60595200-60597400	Weak transcription	Right Ventricle	heart
46	chr5:60595400-60595600	Enhancers	HepG2	liver
47	chr5:60595400-60596400	Weak transcription	Brain Germinal Matrix	brain
48	chr5:60595400-60596400	Weak transcription	NH-A	brain
49	chr5:60595400-60596400	Weak transcription	Osteobl	bone
50	chr5:60595400-60597000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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