Variant report

Variant	rs544979
Chromosome Location	chr3:146186300-146186301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:146185173..146186845-chr3:146259254..146261120,2	K562	blood:
2	chr3:146185354..146186858-chr3:146261288..146263091,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188313	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10804713	0.80[ASN][1000 genomes]
rs10804714	0.82[ASN][1000 genomes]
rs10935626	0.81[ASN][1000 genomes]
rs10935631	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11720256	0.81[ASN][1000 genomes]
rs12053987	0.81[ASN][1000 genomes]
rs12054302	0.81[ASN][1000 genomes]
rs12054308	0.81[ASN][1000 genomes]
rs12054453	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12054455	0.81[ASN][1000 genomes]
rs12107218	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12486656	0.81[ASN][1000 genomes]
rs12486737	0.85[ASN][1000 genomes]
rs12487572	0.96[ASN][1000 genomes]
rs12492503	0.83[ASN][1000 genomes]
rs12494206	0.85[ASN][1000 genomes]
rs12629356	0.81[ASN][1000 genomes]
rs12629420	0.81[ASN][1000 genomes]
rs12633694	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13068178	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13068800	0.85[ASN][1000 genomes]
rs13081634	0.85[ASN][1000 genomes]
rs13088225	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13090489	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13092702	0.81[ASN][1000 genomes]
rs1403640	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1403641	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1403642	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1403643	0.85[ASN][1000 genomes]
rs1403644	0.85[ASN][1000 genomes]
rs1403645	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1523334	0.97[ASN][1000 genomes]
rs1523335	0.82[ASN][1000 genomes]
rs1523336	0.95[ASN][1000 genomes]
rs1608389	0.98[ASN][1000 genomes]
rs1608390	0.96[ASN][1000 genomes]
rs1608392	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17351881	0.87[ASN][1000 genomes]
rs2037565	0.81[ASN][1000 genomes]
rs2091064	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2222465	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2222466	0.85[ASN][1000 genomes]
rs2868438	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34198003	0.81[ASN][1000 genomes]
rs34359311	0.81[ASN][1000 genomes]
rs34535967	0.81[ASN][1000 genomes]
rs34696856	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34740686	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35082616	0.86[ASN][1000 genomes]
rs35223042	0.85[ASN][1000 genomes]
rs35336826	0.85[ASN][1000 genomes]
rs35374128	0.85[ASN][1000 genomes]
rs35695439	0.85[ASN][1000 genomes]
rs4234358	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4282029	0.92[ASN][1000 genomes]
rs4333063	0.84[ASN][1000 genomes]
rs4334615	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4355250	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4380387	0.85[ASN][1000 genomes]
rs4444684	0.85[ASN][1000 genomes]
rs4476473	0.81[ASN][1000 genomes]
rs4558726	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4569626	0.82[ASN][1000 genomes]
rs4572737	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4597678	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4600794	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4681319	0.81[ASN][1000 genomes]
rs4681320	0.81[ASN][1000 genomes]
rs4681321	0.81[ASN][1000 genomes]
rs4681322	0.82[ASN][1000 genomes]
rs4681326	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473517	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs506791	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs509382	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs533756	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs535344	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs544043	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs570781	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs574318	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57545585	0.85[ASN][1000 genomes]
rs6440429	0.81[ASN][1000 genomes]
rs6440430	0.81[ASN][1000 genomes]
rs6440432	0.81[ASN][1000 genomes]
rs6440435	0.82[ASN][1000 genomes]
rs6766583	0.82[ASN][1000 genomes]
rs6774338	0.85[ASN][1000 genomes]
rs6798352	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6801846	0.94[ASN][1000 genomes]
rs6801964	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6806369	0.81[ASN][1000 genomes]
rs692749	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7434147	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7614557	0.81[ASN][1000 genomes]
rs7617214	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7620107	0.81[ASN][1000 genomes]
rs7628445	0.81[ASN][1000 genomes]
rs7633474	0.93[ASN][1000 genomes]
rs7645939	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7646988	0.81[ASN][1000 genomes]
rs7650361	0.81[ASN][1000 genomes]
rs7650546	0.95[ASN][1000 genomes]
rs7653701	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs940193	0.85[ASN][1000 genomes]

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	nsv877618	chr3:146096182-146192324	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv877622	chr3:146131961-146219740	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146181600-146187000	Enhancers	Muscle Satellite Cultured Cells	--
2	chr3:146183000-146187000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:146183000-146187000	Weak transcription	HMEC	breast
4	chr3:146183000-146187000	Weak transcription	NHEK	skin
5	chr3:146183600-146187000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:146184000-146187000	Weak transcription	Right Atrium	heart
7	chr3:146184200-146186800	Weak transcription	Esophagus	oesophagus
8	chr3:146184200-146186800	Weak transcription	Pancreas	Pancrea
9	chr3:146184200-146187000	Weak transcription	Aorta	Aorta
10	chr3:146184200-146187000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:146185200-146186600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:146185600-146186400	Enhancers	A549	lung
13	chr3:146185600-146186400	Enhancers	Osteobl	bone
14	chr3:146185600-146187000	Enhancers	NHDF-Ad	bronchial
15	chr3:146185800-146187000	Enhancers	Fetal Heart	heart
16	chr3:146185800-146187000	Weak transcription	Gastric	stomach
17	chr3:146185800-146187000	Enhancers	Stomach Mucosa	stomach
18	chr3:146185800-146187200	Enhancers	Fetal Lung	lung
19	chr3:146185800-146187200	Weak transcription	Psoas Muscle	Psoas
20	chr3:146185800-146187200	Enhancers	NHLF	lung
21	chr3:146186000-146186400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:146186000-146186400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:146186000-146186600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:146186000-146186600	Enhancers	Hela-S3	cervix
25	chr3:146186000-146187000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:146186000-146187000	Enhancers	Primary hematopoietic stem cells	blood
27	chr3:146186000-146187000	Enhancers	Brain Substantia Nigra	brain
28	chr3:146186200-146186400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:146186200-146186400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr3:146186200-146186600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:146186200-146186600	Enhancers	Fetal Stomach	stomach
32	chr3:146186200-146186800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:146186200-146186800	Enhancers	Brain Hippocampus Middle	brain
34	chr3:146186200-146186800	Enhancers	Fetal Kidney	kidney
35	chr3:146186200-146186800	Active TSS	K562	blood
36	chr3:146186200-146187000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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