Variant report

Variant	rs6414407
Chromosome Location	chr3:162436771-162436772
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10936308	0.88[EUR][1000 genomes]
rs11922500	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11925750	0.88[EUR][1000 genomes]
rs11926645	0.88[EUR][1000 genomes]
rs12489679	0.86[EUR][1000 genomes]
rs13083886	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1874510	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1874512	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1908780	0.84[ASN][1000 genomes]
rs2029925	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2201660	0.84[ASN][1000 genomes]
rs4858910	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4858911	0.83[EUR][1000 genomes]
rs55807361	0.88[EUR][1000 genomes]
rs56242739	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57617609	0.88[EUR][1000 genomes]
rs61170375	0.84[EUR][1000 genomes]
rs62294573	0.88[EUR][1000 genomes]
rs6414403	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441540	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441541	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441543	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764576	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778765	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784170	0.84[ASN][1000 genomes]
rs6795665	0.84[ASN][1000 genomes]
rs6799183	0.84[ASN][1000 genomes]
rs7426713	0.86[EUR][1000 genomes]
rs7426987	0.84[ASN][1000 genomes]
rs7427964	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7427978	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7428118	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7428601	0.84[ASN][1000 genomes]
rs7433902	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7624234	0.86[EUR][1000 genomes]
rs7630042	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7634217	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7646046	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7652373	0.86[EUR][1000 genomes]
rs7652432	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9810012	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9813079	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9815701	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9831314	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9832503	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9839936	0.86[EUR][1000 genomes]
rs9844124	0.87[EUR][1000 genomes]
rs9859307	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9870314	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9874108	0.86[EUR][1000 genomes]
rs9878965	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9882410	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9882755	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006802	chr3:161921063-162599175	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv428424	chr3:162145988-163033943	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1012160	chr3:162182166-162540478	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv592201	chr3:162188625-163142162	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470994	chr3:162217993-162945834	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1005142	chr3:162284967-162447818	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv877758	chr3:162287573-162521339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv877759	chr3:162303276-162521339	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv877761	chr3:162346392-162521339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv592208	chr3:162369863-162437102	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1005637	chr3:162379324-162635451	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv877762	chr3:162400620-162521339	Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv869804	chr3:162414099-162776884	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv829776	chr3:162422424-162577578	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv1001282	chr3:162429561-162513137	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:162432600-162437000	Enhancers	Dnd41	blood
2	chr3:162435800-162439200	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr3:162436000-162437000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr3:162436000-162437200	Enhancers	A549	lung
5	chr3:162436000-162437400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:162436000-162437800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr3:162436000-162439000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr3:162436000-162440200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:162436000-162442200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:162436200-162436800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr3:162436400-162436800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:162436400-162436800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:162436400-162437400	Enhancers	Aorta	Aorta
14	chr3:162436400-162438000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:162436400-162438200	Enhancers	Osteobl	bone
16	chr3:162436400-162442000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:162436600-162436800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr3:162436600-162436800	Enhancers	H9 Cell Line	embryonic stem cell
19	chr3:162436600-162438000	Enhancers	NH-A	brain
20	chr3:162436600-162438200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:162436600-162438200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr3:162436600-162438200	Enhancers	NHDF-Ad	bronchial
23	chr3:162436600-162438400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:162436600-162438400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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