Variant report

Variant	rs1567581
Chromosome Location	chr3:24036406-24036407
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:24033094..24034761-chr3:24035791..24038107,2	K562	blood:
2	chr3:24030711..24032570-chr3:24036287..24038939,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1133926	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1136155	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11706297	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710647	0.97[ASN][1000 genomes]
rs11710679	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11711073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11711380	0.90[ASN][1000 genomes]
rs11713246	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11718625	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11922577	0.82[JPT][hapmap]
rs12497944	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13314607	1.00[ASN][1000 genomes]
rs13318927	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13325754	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1397880	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17787211	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2063481	0.82[JPT][hapmap]
rs2089848	0.82[JPT][hapmap]
rs2361013	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28522849	0.97[ASN][1000 genomes]
rs28623591	0.90[ASN][1000 genomes]
rs34476593	0.90[ASN][1000 genomes]
rs35711415	1.00[ASN][1000 genomes]
rs35886023	0.97[ASN][1000 genomes]
rs4131864	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4568061	0.85[CHB][hapmap]
rs60699428	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61294694	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61645368	0.84[ASN][1000 genomes]
rs62253361	1.00[ASN][1000 genomes]
rs62253380	1.00[ASN][1000 genomes]
rs62253382	1.00[ASN][1000 genomes]
rs62253383	0.91[ASN][1000 genomes]
rs62253387	0.93[ASN][1000 genomes]
rs6550809	0.85[ASN][1000 genomes]
rs6765292	1.00[CHD][hapmap]
rs6778970	0.82[JPT][hapmap]
rs6787216	0.90[ASN][1000 genomes]
rs6789983	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6800407	0.82[JPT][hapmap]
rs73825116	0.84[ASN][1000 genomes]
rs73825124	0.84[ASN][1000 genomes]
rs73825170	0.90[ASN][1000 genomes]
rs73825178	0.90[ASN][1000 genomes]
rs73825181	1.00[ASN][1000 genomes]
rs7629325	1.00[ASN][1000 genomes]
rs7637968	0.82[JPT][hapmap]
rs8933	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs938078	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9815334	0.90[ASN][1000 genomes]
rs9834166	1.00[ASN][1000 genomes]
rs9836860	0.90[ASN][1000 genomes]
rs9836970	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9838694	1.00[ASN][1000 genomes]
rs9850255	0.90[ASN][1000 genomes]
rs9856727	0.94[ASN][1000 genomes]
rs9857442	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9863605	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs9863674	1.00[ASN][1000 genomes]
rs9875213	1.00[ASN][1000 genomes]
rs9876561	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1567581	NR1D2	cis	multi-tissue	Pritchard

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24019600-24040800	Weak transcription	NHLF	lung
2	chr3:24030800-24040400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:24032200-24036600	Enhancers	Fetal Stomach	stomach
4	chr3:24032800-24036800	Enhancers	Fetal Heart	heart
5	chr3:24033600-24039000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:24033600-24040600	Weak transcription	Primary B cells from cord blood	blood
7	chr3:24033800-24036600	Enhancers	Primary hematopoietic stem cells	blood
8	chr3:24033800-24040600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:24034200-24036800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:24034200-24039000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:24034600-24037200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:24034600-24040400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:24035200-24040600	Weak transcription	Brain Anterior Caudate	brain
14	chr3:24035400-24037400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:24035600-24036600	Enhancers	Right Ventricle	heart
16	chr3:24035800-24037400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr3:24035800-24040400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:24035800-24040600	Weak transcription	Brain Angular Gyrus	brain
19	chr3:24036000-24037200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:24036000-24037200	Weak transcription	Fetal Lung	lung
21	chr3:24036000-24038200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:24036000-24040400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:24036000-24040400	Weak transcription	HSMMtube	muscle
24	chr3:24036000-24040400	Weak transcription	NHDF-Ad	bronchial
25	chr3:24036000-24040600	Weak transcription	Brain Germinal Matrix	brain
26	chr3:24036000-24040600	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:24036000-24040600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:24036000-24040600	Weak transcription	Brain Substantia Nigra	brain
29	chr3:24036000-24040800	Weak transcription	Ovary	ovary
30	chr3:24036000-24053400	Weak transcription	Psoas Muscle	Psoas
31	chr3:24036200-24040400	Weak transcription	Adipose Nuclei	Adipose
32	chr3:24036200-24040600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:24036200-24040600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:24036200-24040600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:24036200-24040600	Weak transcription	Fetal Kidney	kidney
36	chr3:24036200-24040600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:24036200-24040600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:24036200-24040800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:24036400-24040400	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:24036400-24040800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:24036400-24043600	Weak transcription	Aorta	Aorta

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