Variant report

Variant	rs6662443
Chromosome Location	chr1:227285073-227285074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1007574	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10495260	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10495267	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799383	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10799384	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10799391	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10799396	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10799397	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916083	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916084	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916085	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916086	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916089	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916090	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916092	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916097	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12026688	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031609	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12035986	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12036915	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044287	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12047828	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12073220	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125514	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12129006	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135061	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12140758	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12141869	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12563165	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12565056	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12742066	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1304324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1320490	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464079	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1913344	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1929868	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1929869	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2095016	0.85[ASN][1000 genomes]
rs34708504	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3818694	0.80[ASN][1000 genomes]
rs4512610	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653797	0.83[EUR][1000 genomes]
rs56260717	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674641	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6682849	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6684284	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6684433	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6685954	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72750172	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7529970	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9887962	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1011654	chr1:227196502-227308416	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv873239	chr1:227222125-227361072	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv468227	chr1:227223736-227340790	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv549269	chr1:227223736-227340790	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv873240	chr1:227228946-227361072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv873241	chr1:227242247-227361072	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227209200-227301600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
4	chr1:227216800-227287600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:227220600-227288000	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:227226800-227285600	Weak transcription	Brain Germinal Matrix	brain
7	chr1:227236000-227286200	Weak transcription	Fetal Brain Male	brain
8	chr1:227240000-227286800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:227247400-227299800	Weak transcription	HMEC	breast
10	chr1:227251000-227300000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:227257600-227288000	Weak transcription	HSMMtube	muscle
12	chr1:227257800-227312200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
14	chr1:227260400-227287800	Weak transcription	NHEK	skin
15	chr1:227261400-227287800	Weak transcription	Osteobl	bone
16	chr1:227268800-227287000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:227271800-227286600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:227271800-227286800	Weak transcription	NHDF-Ad	bronchial
19	chr1:227271800-227287800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:227271800-227288000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:227271800-227299600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:227272000-227285800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:227272600-227286400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:227272600-227294400	Weak transcription	Fetal Heart	heart
25	chr1:227272800-227285200	Weak transcription	Psoas Muscle	Psoas
26	chr1:227272800-227295000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:227272800-227295000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:227272800-227331000	Weak transcription	Lung	lung
29	chr1:227273000-227286400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:227273000-227312400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:227274600-227285200	Weak transcription	Left Ventricle	heart
32	chr1:227275400-227287000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:227275800-227302600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr1:227277000-227288600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:227277200-227286400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:227277200-227302600	Weak transcription	Brain Substantia Nigra	brain
37	chr1:227279200-227286000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:227279200-227286000	Weak transcription	Adipose Nuclei	Adipose
39	chr1:227279200-227286200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:227279200-227286400	Weak transcription	Ovary	ovary
41	chr1:227279200-227286600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:227279200-227286600	Weak transcription	Fetal Lung	lung
43	chr1:227279200-227287000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:227279200-227287800	Weak transcription	Aorta	Aorta
45	chr1:227279200-227287800	Weak transcription	Brain Anterior Caudate	brain
46	chr1:227279200-227287800	Weak transcription	Fetal Stomach	stomach
47	chr1:227279400-227285200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:227279400-227286600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:227279400-227286800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:227279400-227288000	Weak transcription	NH-A	brain

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