Variant report

Variant	rs6542838
Chromosome Location	chr2:99452458-99452459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99352944..99355702-chr2:99450894..99453779,2	MCF-7	breast:
2	chr2:99266174..99266704-chr2:99452319..99452854,2	MCF-7	breast:
3	chr2:99028647..99029579-chr2:99452420..99452934,2	K562	blood:
4	chr2:99344923..99349258-chr2:99450100..99455296,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10169003	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10172158	0.88[EUR][1000 genomes]
rs10181972	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10188156	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123755	0.88[EUR][1000 genomes]
rs11887536	0.88[EUR][1000 genomes]
rs11893888	0.82[EUR][1000 genomes]
rs12468024	0.88[EUR][1000 genomes]
rs12712033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12712034	0.90[CHB][hapmap]
rs12712035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712036	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes]
rs12712038	0.88[EUR][1000 genomes]
rs12712039	0.86[EUR][1000 genomes]
rs12992214	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13004923	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13389386	0.90[JPT][hapmap]
rs1356424	0.88[CEU][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1568213	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1581250	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1581251	0.88[EUR][1000 genomes]
rs1878585	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1983352	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276604	0.85[JPT][hapmap]
rs2280256	0.88[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4263159	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4850888	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851162	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851163	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851167	0.88[EUR][1000 genomes]
rs4851170	0.88[EUR][1000 genomes]
rs4851171	0.87[EUR][1000 genomes]
rs6542839	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes]
rs6711022	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6713991	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6714243	0.88[EUR][1000 genomes]
rs6717372	0.85[EUR][1000 genomes]
rs6719634	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes]
rs6726156	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6733011	0.98[ASN][1000 genomes]
rs6757099	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7579189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7581128	0.81[JPT][hapmap]
rs7608889	0.81[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs925887	0.80[EUR][1000 genomes]
rs981601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs981602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99440000-99460600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:99440400-99453800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:99440400-99463400	Weak transcription	Fetal Intestine Large	intestine
4	chr2:99440600-99453800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:99448400-99454000	Enhancers	Fetal Thymus	thymus
6	chr2:99449400-99454000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:99450000-99454600	Weak transcription	Brain Angular Gyrus	brain
8	chr2:99450000-99468400	Weak transcription	Fetal Intestine Small	intestine
9	chr2:99450400-99453800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr2:99450600-99453600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr2:99450600-99455200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:99450600-99455200	Weak transcription	HMEC	breast
13	chr2:99450600-99456200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:99450800-99452600	Weak transcription	Adipose Nuclei	Adipose
15	chr2:99450800-99452800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:99450800-99453600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:99450800-99462800	Weak transcription	Gastric	stomach
18	chr2:99451000-99453400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:99451000-99456400	Weak transcription	Lung	lung
20	chr2:99451200-99454000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr2:99451400-99453200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr2:99451400-99454000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr2:99451600-99454000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr2:99451600-99454000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr2:99451800-99452600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:99451800-99453200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr2:99451800-99453400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr2:99451800-99454000	Enhancers	Brain Anterior Caudate	brain
29	chr2:99452000-99453400	Enhancers	Primary T cells from cord blood	blood
30	chr2:99452000-99454000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:99452200-99453200	Strong transcription	Esophagus	oesophagus
32	chr2:99452200-99453200	Flanking Active TSS	Dnd41	blood
33	chr2:99452200-99453200	Enhancers	HepG2	liver
34	chr2:99452400-99452600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr2:99452400-99452800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr2:99452400-99452800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:99452400-99453200	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr2:99452400-99453200	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr2:99452400-99453800	Weak transcription	HUVEC	blood vessel

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