Variant report

Variant	rs6576765
Chromosome Location	chr1:85871012-85871013
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1001604	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10489513	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11161606	0.81[CEU][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap]
rs11161607	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11161610	0.83[EUR][1000 genomes]
rs11161611	0.89[CEU][hapmap];0.80[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1146379	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1146382	0.85[CEU][hapmap]
rs12044537	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12047422	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12124170	0.84[EUR][1000 genomes]
rs12125557	0.90[EUR][1000 genomes]
rs12140103	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1498373	0.85[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs1498375	0.83[EUR][1000 genomes]
rs1554597	0.89[CEU][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs173026	0.83[EUR][1000 genomes]
rs18582	0.85[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes]
rs1884139	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2011825	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2012683	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2037594	0.80[LWK][hapmap];0.83[MKK][hapmap];0.81[YRI][hapmap]
rs2177461	0.88[CEU][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2207368	0.87[CEU][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2268667	0.85[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs2300634	0.85[CEU][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs2300637	0.84[EUR][1000 genomes]
rs233047	0.85[CEU][hapmap];0.80[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs233050	0.89[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs233053	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs233054	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs233055	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233057	0.83[EUR][1000 genomes]
rs233058	0.83[EUR][1000 genomes]
rs233059	0.83[EUR][1000 genomes]
rs233060	0.83[EUR][1000 genomes]
rs233061	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233062	0.83[EUR][1000 genomes]
rs233066	0.84[EUR][1000 genomes]
rs233067	0.84[EUR][1000 genomes]
rs233068	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233069	0.85[EUR][1000 genomes]
rs233071	0.85[EUR][1000 genomes]
rs233072	0.83[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs233091	0.85[EUR][1000 genomes]
rs233093	0.85[CEU][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.84[EUR][1000 genomes]
rs233095	0.84[EUR][1000 genomes]
rs233097	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233099	0.85[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs233108	0.83[EUR][1000 genomes]
rs233109	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233112	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233113	0.85[CEU][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs233114	0.83[EUR][1000 genomes]
rs233115	0.84[CEU][hapmap];0.93[GIH][hapmap];0.83[EUR][1000 genomes]
rs233118	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233119	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs233120	0.82[EUR][1000 genomes]
rs233121	0.83[EUR][1000 genomes]
rs233124	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233127	0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs233130	0.96[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs233131	0.83[EUR][1000 genomes]
rs233132	0.83[EUR][1000 genomes]
rs233133	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2474123	0.89[CEU][hapmap];0.81[MKK][hapmap];0.82[AMR][1000 genomes]
rs2892888	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3087894	0.83[EUR][1000 genomes]
rs3768227	0.85[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes]
rs3949301	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs423105	0.83[EUR][1000 genomes]
rs4949890	0.84[EUR][1000 genomes]
rs4949900	0.89[CEU][hapmap];0.80[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs506082	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6576763	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6576764	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6576766	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6576767	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6657732	0.89[GIH][hapmap]
rs6657817	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6671599	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66811655	0.83[EUR][1000 genomes]
rs669173	0.83[GIH][hapmap]
rs6697083	0.81[CEU][hapmap]
rs6704103	0.89[CEU][hapmap];0.80[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67611930	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72724606	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7525786	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs761601	0.85[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes]
rs997251	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	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
4	esv3393958	chr1:85857980-85874598	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85856000-85872800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:85862200-85874600	Weak transcription	Pancreas	Pancrea
3	chr1:85864000-85872600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:85864400-85871800	Weak transcription	NH-A	brain
5	chr1:85864400-85872200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:85864400-85873000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:85864400-85874600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:85864800-85876800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:85865200-85871200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:85865400-85871200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:85865400-85871400	Weak transcription	Fetal Lung	lung
12	chr1:85865400-85871400	Weak transcription	HSMM	muscle
13	chr1:85865400-85872800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:85865600-85871600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:85866200-85871600	Weak transcription	Adipose Nuclei	Adipose
16	chr1:85868600-85872800	Enhancers	Liver	Liver
17	chr1:85869000-85871200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr1:85869000-85872800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:85869200-85873200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:85869400-85872200	Weak transcription	Fetal Kidney	kidney
21	chr1:85869800-85871600	Enhancers	Aorta	Aorta
22	chr1:85869800-85871800	Enhancers	Colon Smooth Muscle	Colon
23	chr1:85869800-85874400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:85870000-85871200	Weak transcription	Brain Substantia Nigra	brain
25	chr1:85870000-85871800	Enhancers	Ovary	ovary
26	chr1:85870000-85873000	Enhancers	HSMMtube	muscle
27	chr1:85870200-85872600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:85870200-85874800	Enhancers	Osteobl	bone
29	chr1:85870400-85872800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:85870400-85872800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:85870600-85871400	Enhancers	Fetal Muscle Leg	muscle
32	chr1:85870600-85871800	Enhancers	Fetal Stomach	stomach
33	chr1:85870600-85872800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:85870600-85872800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:85870800-85871600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:85870800-85871800	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr1:85870800-85872000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:85870800-85872600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:85870800-85872600	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr1:85870800-85872800	Enhancers	NHDF-Ad	bronchial
41	chr1:85871000-85871400	Enhancers	Brain Anterior Caudate	brain
42	chr1:85871000-85871600	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr1:85871000-85871800	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr1:85871000-85871800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr1:85871000-85872200	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr1:85871000-85872200	Genic enhancers	HUVEC	blood vessel
47	chr1:85871000-85872800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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