Variant report

Variant	rs6447541
Chromosome Location	chr4:47215939-47215940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10002281	0.84[ASW][hapmap];0.81[LWK][hapmap];0.81[YRI][hapmap]
rs10003607	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10009164	0.93[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs10010157	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10016815	0.94[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs10016894	0.94[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs10017326	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs10017723	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap]
rs10018597	0.95[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes]
rs10025516	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs10029262	0.81[YRI][hapmap]
rs10517179	0.84[ASW][hapmap]
rs10805153	0.88[CHB][hapmap]
rs11727759	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap]
rs11931599	0.90[ASN][1000 genomes]
rs12502993	0.88[CHB][hapmap]
rs12640095	0.84[LWK][hapmap]
rs12645665	0.84[LWK][hapmap]
rs1372497	0.94[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs1372498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372499	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1442091	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap]
rs1442108	0.94[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs1442109	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap]
rs1470208	0.94[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs1530302	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1583952	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs16860067	0.90[ASN][1000 genomes]
rs16860071	0.90[ASN][1000 genomes]
rs16860083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860087	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17600029	0.84[ASW][hapmap];0.84[LWK][hapmap];0.81[YRI][hapmap]
rs17600169	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2351299	0.84[LWK][hapmap]
rs2351300	0.84[ASW][hapmap];0.84[LWK][hapmap];0.81[YRI][hapmap]
rs28482891	0.90[ASN][1000 genomes]
rs28498348	0.90[ASN][1000 genomes]
rs28587597	0.89[ASN][1000 genomes]
rs28605268	0.94[EUR][1000 genomes]
rs28663255	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098797	0.94[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs3098799	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs3098802	0.88[CHB][hapmap]
rs3114084	0.88[CHB][hapmap]
rs3114088	0.88[CHB][hapmap]
rs3114089	0.88[CHB][hapmap]
rs34457317	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822110	0.84[ASW][hapmap]
rs4403026	0.88[CHB][hapmap]
rs4426746	0.88[CHB][hapmap]
rs4481218	0.94[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs4586906	0.88[CHB][hapmap]
rs4695200	0.87[ASN][1000 genomes]
rs4695201	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs4695202	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs55807683	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6834646	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7435958	0.84[ASW][hapmap];0.84[LWK][hapmap];0.81[YRI][hapmap]
rs7666487	0.94[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs7671741	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7673824	0.81[YRI][hapmap]
rs7695365	0.94[CHB][hapmap];0.81[JPT][hapmap]

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	nsv829922	chr4:47093785-47261181	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv879003	chr4:47102993-47215939	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv1009766	chr4:47155845-47277391	Enhancers Flanking Active TSS Weak transcription Active TSS	lncRNA	n/a	inside rSNPs	diseases
4	nsv998919	chr4:47207023-47476876	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47211600-47217400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr4:47211800-47216200	Weak transcription	NHLF	lung
3	chr4:47212000-47216200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:47212000-47216200	Weak transcription	HSMMtube	muscle
5	chr4:47213200-47216200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:47213200-47216200	Weak transcription	HMEC	breast
7	chr4:47213200-47216400	Weak transcription	HSMM	muscle
8	chr4:47214200-47218400	Enhancers	NH-A	brain
9	chr4:47214400-47216200	Enhancers	Placenta Amnion	Placenta Amnion
10	chr4:47214600-47216000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:47214600-47226600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:47214800-47216000	Enhancers	Brain Cingulate Gyrus	brain
13	chr4:47215000-47216200	Enhancers	Osteobl	bone
14	chr4:47215000-47216600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr4:47215000-47218400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr4:47215200-47216200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:47215200-47216600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:47215400-47216200	Active TSS	Brain Substantia Nigra	brain
19	chr4:47215400-47216600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:47215600-47216000	Active TSS	Brain Angular Gyrus	brain
21	chr4:47215600-47216000	Active TSS	Brain Anterior Caudate	brain
22	chr4:47215600-47216400	Enhancers	Fetal Heart	heart
23	chr4:47215600-47217200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr4:47215800-47216000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:47215800-47216000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:47215800-47216200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:47215800-47216400	Enhancers	Brain Germinal Matrix	brain
28	chr4:47215800-47216400	Active TSS	Brain Hippocampus Middle	brain
29	chr4:47215800-47216600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:47215800-47217400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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