Variant report

Variant	rs233071
Chromosome Location	chr1:85806005-85806006
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1001604	0.85[EUR][1000 genomes]
rs10489513	0.83[EUR][1000 genomes]
rs11161607	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11161610	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11161611	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12044537	0.86[EUR][1000 genomes]
rs12047422	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12124170	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12125557	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12140103	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1498373	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1498375	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1554597	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs173026	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs18582	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1884139	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2011825	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2012683	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2177461	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2207368	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2268667	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2300634	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2300637	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs233047	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233050	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs233053	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs233054	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233055	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs233057	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233058	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233059	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233060	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233061	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs233062	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233066	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233067	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233068	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs233069	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233072	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs233074	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233091	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233093	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233095	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs233097	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs233099	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233108	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233109	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs233112	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs233113	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233114	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233115	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233118	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs233119	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233120	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233121	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233124	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs233127	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233130	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233131	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233132	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233133	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2892888	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3087894	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3768227	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3949301	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs423105	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949890	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949900	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6576763	0.84[EUR][1000 genomes]
rs6576764	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6576765	0.85[EUR][1000 genomes]
rs6576766	0.81[EUR][1000 genomes]
rs6576767	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6657817	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6671599	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66811655	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6704103	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67611930	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72724606	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs761601	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs997251	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85796600-85809400	Weak transcription	Stomach Mucosa	stomach
2	chr1:85796800-85806400	Weak transcription	Small Intestine	intestine
3	chr1:85796800-85809600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:85798400-85806200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:85798800-85808400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:85798800-85808400	Weak transcription	Ovary	ovary
7	chr1:85798800-85824800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:85798800-85824800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:85799000-85813600	Weak transcription	Fetal Intestine Large	intestine
10	chr1:85800400-85808800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:85800400-85815000	Weak transcription	Fetal Intestine Small	intestine
12	chr1:85800800-85807600	Weak transcription	HSMMtube	muscle
13	chr1:85803400-85807000	Enhancers	Hela-S3	cervix
14	chr1:85803600-85806800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr1:85803600-85807200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:85803600-85807800	Genic enhancers	Osteobl	bone
17	chr1:85803600-85808600	Enhancers	HUVEC	blood vessel
18	chr1:85804200-85806200	Enhancers	NHEK	skin
19	chr1:85804200-85807600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:85804200-85808600	Genic enhancers	HSMM	muscle
21	chr1:85804400-85806800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:85804600-85806200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:85804800-85811000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:85805000-85806200	Enhancers	A549	lung
25	chr1:85805000-85806600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:85805000-85806800	Enhancers	Adipose Nuclei	Adipose
27	chr1:85805000-85807000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:85805000-85807000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:85805000-85808000	Genic enhancers	NHDF-Ad	bronchial
30	chr1:85805200-85806400	Enhancers	Pancreas	Pancrea
31	chr1:85805200-85807000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:85805200-85809000	Weak transcription	Fetal Heart	heart
33	chr1:85805400-85806600	Enhancers	Colon Smooth Muscle	Colon
34	chr1:85805400-85807600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:85805400-85808400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:85805600-85806400	Enhancers	Rectal Smooth Muscle	rectum
37	chr1:85805600-85806800	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr1:85805600-85807000	Enhancers	NH-A	brain
39	chr1:85805600-85807600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:85805600-85807600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:85805600-85807800	Weak transcription	HMEC	breast
42	chr1:85805600-85807800	Weak transcription	NHLF	lung
43	chr1:85805600-85808400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:85805800-85806200	Genic enhancers	HepG2	liver
45	chr1:85805800-85806400	Weak transcription	Aorta	Aorta
46	chr1:85805800-85806600	Enhancers	Left Ventricle	heart
47	chr1:85805800-85806800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:85805800-85806800	Enhancers	Fetal Muscle Leg	muscle
49	chr1:85805800-85806800	Enhancers	Psoas Muscle	Psoas
50	chr1:85805800-85807600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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