Variant report

Variant	rs6657817
Chromosome Location	chr1:85874614-85874615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1001604	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1006989	0.86[AFR][1000 genomes]
rs10489513	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10747318	0.88[AFR][1000 genomes]
rs10782549	0.91[AFR][1000 genomes]
rs10873701	0.88[AFR][1000 genomes]
rs10873702	0.84[AFR][1000 genomes]
rs11161606	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11161607	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161610	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161611	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1146379	0.83[EUR][1000 genomes]
rs12044537	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12047422	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12124170	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12125557	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12140103	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1357635	0.90[AFR][1000 genomes]
rs1498373	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1498375	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1523995	0.88[AFR][1000 genomes]
rs1554597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1608537	0.91[AFR][1000 genomes]
rs173026	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs18582	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1884139	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1965876	0.91[AFR][1000 genomes]
rs2011825	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2012683	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2016104	0.92[AFR][1000 genomes]
rs2177461	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207368	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2268667	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300634	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300637	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs233047	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233050	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233053	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs233054	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233057	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233058	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233059	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233060	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233061	0.84[EUR][1000 genomes]
rs233062	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs233066	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233067	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233068	0.85[EUR][1000 genomes]
rs233069	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233071	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233072	0.85[EUR][1000 genomes]
rs233074	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs233091	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233093	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233095	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs233097	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs233099	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233108	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233109	0.84[EUR][1000 genomes]
rs233112	0.83[EUR][1000 genomes]
rs233113	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233114	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233115	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233118	0.83[EUR][1000 genomes]
rs233119	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233120	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233121	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233124	0.83[EUR][1000 genomes]
rs233127	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233130	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233131	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233132	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233133	0.84[EUR][1000 genomes]
rs2389948	0.80[AFR][1000 genomes]
rs2840319	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2892888	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087894	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3768227	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3920521	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3949301	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs423105	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4428939	0.83[AFR][1000 genomes]
rs4949890	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4949900	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506082	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs539714	0.80[AFR][1000 genomes]
rs6420965	0.89[AFR][1000 genomes]
rs6576761	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6576763	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6576764	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576765	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6576766	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6576767	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671599	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6672870	0.81[AFR][1000 genomes]
rs66811655	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6704103	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67611930	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72724606	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72724608	0.87[AFR][1000 genomes]
rs729655	0.85[AMR][1000 genomes]
rs7515261	0.88[AFR][1000 genomes]
rs7539738	0.86[AFR][1000 genomes]
rs7546931	0.83[AFR][1000 genomes]
rs7547571	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs761601	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs997251	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[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	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	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85864800-85876800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:85870200-85874800	Enhancers	Osteobl	bone
3	chr1:85871400-85878400	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:85871600-85876600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:85871800-85877000	Weak transcription	Ovary	ovary
6	chr1:85872000-85877200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:85872800-85874800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:85873000-85875400	Enhancers	Brain Anterior Caudate	brain
9	chr1:85873200-85876000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:85873200-85879600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:85873400-85874800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:85873400-85874800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:85873400-85875400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:85873400-85876800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:85873400-85876800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:85873400-85882800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:85873600-85875000	Enhancers	HUVEC	blood vessel
18	chr1:85873600-85885000	Weak transcription	Fetal Intestine Large	intestine
19	chr1:85873800-85875400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:85873800-85875400	Enhancers	Liver	Liver
21	chr1:85873800-85876600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:85873800-85876800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:85873800-85882000	Weak transcription	Fetal Intestine Small	intestine
24	chr1:85873800-85885400	Weak transcription	Fetal Stomach	stomach
25	chr1:85873800-85887600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:85874000-85875200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:85874000-85875400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:85874000-85876600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:85874000-85876800	Weak transcription	HSMM	muscle
30	chr1:85874000-85877000	Weak transcription	NHDF-Ad	bronchial
31	chr1:85874000-85877400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:85874000-85878000	Weak transcription	Stomach Mucosa	stomach
33	chr1:85874000-85903800	Weak transcription	NHLF	lung
34	chr1:85874200-85903600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:85874400-85875200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:85874400-85877000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:85874400-85903600	Weak transcription	HepG2	liver
38	chr1:85874400-85904200	Weak transcription	NH-A	brain
39	chr1:85874600-85875000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:85874600-85875400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:85874600-85876000	Enhancers	Pancreas	Pancrea
42	chr1:85874600-85876600	Weak transcription	HSMMtube	muscle
43	chr1:85874600-85877200	Weak transcription	Aorta	Aorta

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