Variant report

Variant	rs12658023
Chromosome Location	chr5:127296394-127296395
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:127294744..127297859-chr5:127418074..127420896,5	MCF-7	breast:
2	chr5:127292969..127298749-chr5:127417448..127421101,7	MCF-7	breast:
3	chr5:127216714..127218320-chr5:127295438..127298339,2	MCF-7	breast:
4	chr5:127291358..127294527-chr5:127295144..127299558,4	K562	blood:

Variant related genes	Relation type
ENSG00000064651	Chromatin interaction
ENSG00000245937	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10037914	0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10065448	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10072806	0.83[JPT][hapmap]
rs10074995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10079317	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];0.98[ASN][1000 genomes]
rs10463834	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10478787	0.84[JPT][hapmap]
rs10900794	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11740438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11740439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741283	0.94[ASN][1000 genomes]
rs12517005	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12523625	0.84[JPT][hapmap]
rs12653621	0.86[ASN][1000 genomes]
rs13361741	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];0.98[ASN][1000 genomes]
rs1520246	1.00[JPT][hapmap]
rs2286386	0.80[ASN][1000 genomes]
rs2409037	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs28473744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28542972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28567046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28591675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28636438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28687461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28736542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28816429	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4836345	1.00[JPT][hapmap]
rs55896045	0.94[ASN][1000 genomes]
rs6877403	0.94[ASN][1000 genomes]
rs6892704	0.84[JPT][hapmap]
rs6898956	0.94[ASN][1000 genomes]
rs732236	0.84[JPT][hapmap]
rs9327457	1.00[JPT][hapmap]
rs9327458	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127285800-127303800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr5:127287400-127297200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr5:127290600-127332000	Weak transcription	Aorta	Aorta
4	chr5:127290800-127297400	Weak transcription	Spleen	Spleen
5	chr5:127292200-127297600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr5:127292400-127296400	Enhancers	Left Ventricle	heart
7	chr5:127292600-127296400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr5:127292600-127296400	Enhancers	HepG2	liver
9	chr5:127292600-127298400	Enhancers	Fetal Intestine Large	intestine
10	chr5:127292600-127298600	Enhancers	Fetal Intestine Small	intestine
11	chr5:127292800-127296400	Enhancers	Brain Hippocampus Middle	brain
12	chr5:127292800-127297200	Enhancers	Fetal Lung	lung
13	chr5:127292800-127297600	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr5:127292800-127297800	Enhancers	HUVEC	blood vessel
15	chr5:127292800-127298400	Enhancers	Fetal Heart	heart
16	chr5:127292800-127314400	Weak transcription	Pancreas	Pancrea
17	chr5:127293000-127297600	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr5:127293000-127298600	Enhancers	Stomach Mucosa	stomach
19	chr5:127293200-127297400	Weak transcription	Gastric	stomach
20	chr5:127293200-127301800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:127293200-127301800	Weak transcription	Ovary	ovary
22	chr5:127293200-127303600	Weak transcription	Esophagus	oesophagus
23	chr5:127293400-127297200	Weak transcription	Right Atrium	heart
24	chr5:127293600-127301800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:127294000-127296400	Enhancers	Fetal Thymus	thymus
26	chr5:127294200-127297200	Enhancers	Dnd41	blood
27	chr5:127294200-127297600	Enhancers	Adipose Nuclei	Adipose
28	chr5:127294200-127297600	Enhancers	Rectal Smooth Muscle	rectum
29	chr5:127294400-127296400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:127294400-127302800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:127294600-127296400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:127294600-127296400	Enhancers	Hela-S3	cervix
33	chr5:127294600-127296400	Enhancers	HMEC	breast
34	chr5:127294600-127296400	Enhancers	NHEK	skin
35	chr5:127294800-127296400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:127294800-127296400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr5:127294800-127297000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr5:127294800-127297200	Weak transcription	Thymus	Thymus
39	chr5:127295000-127296400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:127295000-127296800	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr5:127295000-127297800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:127295000-127297800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:127295000-127298000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr5:127295000-127298400	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr5:127295200-127296400	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr5:127295200-127296600	Enhancers	Fetal Muscle Leg	muscle
47	chr5:127295200-127296600	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr5:127295200-127297800	Enhancers	Primary T cells from cord blood	blood
49	chr5:127295200-127298400	Enhancers	Small Intestine	intestine
50	chr5:127295200-127298600	Enhancers	Rectal Mucosa Donor 31	rectum

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