Variant report

Variant	rs566576
Chromosome Location	chr1:92647861-92647862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10747411	1.00[ASN][1000 genomes]
rs10782838	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10875348	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs11166568	1.00[ASN][1000 genomes]
rs11166575	1.00[ASN][1000 genomes]
rs1226177	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226188	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1234874	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1386585	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs1487537	1.00[ASN][1000 genomes]
rs1487539	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs17131594	1.00[CHB][hapmap]
rs17131596	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17131767	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1748178	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17519833	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1825813	1.00[ASN][1000 genomes]
rs1906279	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2025607	1.00[ASN][1000 genomes]
rs2046621	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2391139	1.00[ASN][1000 genomes]
rs2391140	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2763040	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3103177	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs3103180	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs3122320	1.00[ASN][1000 genomes]
rs3131815	1.00[ASN][1000 genomes]
rs3131816	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs3131824	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs3131831	1.00[ASN][1000 genomes]
rs3862907	1.00[CHB][hapmap]
rs4247165	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs475034	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476490	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs481384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs481677	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs487443	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs495446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs501786	0.86[AFR][1000 genomes]
rs501872	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs510857	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs517404	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs523692	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs524989	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs530815	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs532031	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs533124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs537754	1.00[ASN][1000 genomes]
rs538054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541168	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs544556	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs548100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs548141	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552468	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs553173	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs562119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs564077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs566702	0.82[AMR][1000 genomes]
rs579668	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6603963	1.00[ASN][1000 genomes]
rs6603967	1.00[ASN][1000 genomes]
rs6604089	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6604091	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6664544	1.00[CHB][hapmap]
rs6668529	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6668685	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6692060	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs6696071	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6700124	1.00[CHB][hapmap]
rs7512301	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs7520275	1.00[CHB][hapmap]
rs7542747	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs7545445	1.00[ASN][1000 genomes]
rs9659484	1.00[CHB][hapmap]
rs974924	0.86[AFR][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	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv871508	chr1:92478130-92781579	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv546821	chr1:92525678-92650349	ZNF genes & repeats Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92609800-92651200	Weak transcription	Fetal Kidney	kidney
2	chr1:92625000-92648200	Weak transcription	Fetal Stomach	stomach
3	chr1:92625600-92651000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:92626200-92652000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:92626600-92648400	Weak transcription	Fetal Intestine Small	intestine
6	chr1:92626600-92650800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:92626600-92657400	Weak transcription	Right Ventricle	heart
8	chr1:92626800-92650000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:92626800-92651400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:92627800-92648200	Weak transcription	Lung	lung
11	chr1:92628000-92648600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:92628200-92651800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:92632800-92648800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:92633800-92649400	Weak transcription	HSMMtube	muscle
15	chr1:92635200-92650400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:92635600-92648400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:92636200-92651000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:92636800-92652400	Weak transcription	Fetal Brain Female	brain
19	chr1:92640200-92650200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:92640400-92649800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:92642400-92662600	Weak transcription	NHDF-Ad	bronchial
22	chr1:92645000-92648800	Weak transcription	Fetal Heart	heart
23	chr1:92645400-92649800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:92645600-92649200	Weak transcription	Dnd41	blood
25	chr1:92645600-92650400	Weak transcription	Thymus	Thymus
26	chr1:92645800-92648000	Strong transcription	Primary T cells from cord blood	blood
27	chr1:92645800-92648000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:92645800-92648000	Strong transcription	Adipose Nuclei	Adipose
29	chr1:92645800-92648000	Strong transcription	Brain Substantia Nigra	brain
30	chr1:92645800-92648200	Strong transcription	Left Ventricle	heart
31	chr1:92645800-92650200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:92646400-92652000	Weak transcription	Psoas Muscle	Psoas
33	chr1:92646600-92648000	Strong transcription	Fetal Lung	lung
34	chr1:92646600-92651400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:92646600-92652200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:92646800-92648000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:92646800-92651000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:92646800-92652000	Weak transcription	Fetal Intestine Large	intestine
39	chr1:92647000-92648600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:92647000-92649400	Weak transcription	Brain Germinal Matrix	brain
41	chr1:92647000-92651400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:92647200-92648800	Weak transcription	Aorta	Aorta
43	chr1:92647200-92648800	Weak transcription	Pancreas	Pancrea
44	chr1:92647200-92649400	Weak transcription	Ovary	ovary
45	chr1:92647200-92649600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:92647200-92649600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:92647200-92652000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:92647200-92653600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:92647200-92655800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:92647400-92649000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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