Variant report

Variant	rs4973329
Chromosome Location	chr2:231405572-231405573
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11687978	0.87[ASN][1000 genomes]
rs1615764	0.83[ASN][1000 genomes]
rs1649893	0.95[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs1649895	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1649923	0.90[ASN][1000 genomes]
rs1678152	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1678157	0.85[ASN][1000 genomes]
rs1678158	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678175	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678186	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1678188	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1678196	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1678197	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1678208	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2559092	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4972956	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55736462	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62193429	0.85[ASN][1000 genomes]
rs62193432	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6711920	0.85[ASN][1000 genomes]
rs6712053	0.85[ASN][1000 genomes]
rs6740413	0.85[ASN][1000 genomes]
rs699662	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs699663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836230	0.87[ASN][1000 genomes]
rs836231	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs836233	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs836234	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836235	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs856838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860704	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs866270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv875948	chr2:231380697-231420401	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv584673	chr2:231385231-231433237	Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4973329	TIGD1	cis	cerebellum	SCAN
rs4973329	UGT1A1	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231371000-231409800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:231390600-231408200	Weak transcription	Esophagus	oesophagus
3	chr2:231390800-231405600	Weak transcription	Thymus	Thymus
4	chr2:231390800-231409200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:231391000-231406400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:231398000-231405600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:231398400-231406200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr2:231401000-231430200	Weak transcription	Pancreas	Pancrea
9	chr2:231401400-231408600	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:231401800-231406400	Weak transcription	Osteobl	bone
11	chr2:231401800-231409200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:231402200-231406200	Weak transcription	Right Ventricle	heart
13	chr2:231402600-231406000	Weak transcription	Liver	Liver
14	chr2:231402800-231405600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:231402800-231405600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:231402800-231405600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:231402800-231406000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:231403000-231405600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:231403200-231406600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:231403200-231410200	Strong transcription	Primary B cells from cord blood	blood
21	chr2:231403600-231405600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:231403600-231407800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:231403600-231408600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:231403800-231405600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:231403800-231406800	Strong transcription	Ovary	ovary
26	chr2:231403800-231408800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr2:231403800-231409600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:231404000-231405600	ZNF genes & repeats	Lung	lung
29	chr2:231404000-231406800	ZNF genes & repeats	Aorta	Aorta
30	chr2:231404000-231406800	Strong transcription	Spleen	Spleen
31	chr2:231404000-231407200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:231404000-231407200	Strong transcription	Left Ventricle	heart
33	chr2:231404000-231408400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:231404000-231409000	Strong transcription	Primary T cells from cord blood	blood
35	chr2:231404000-231409000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr2:231404000-231417200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:231404200-231405800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:231404200-231406400	Genic enhancers	GM12878-XiMat	blood
39	chr2:231404200-231409000	Strong transcription	Adipose Nuclei	Adipose
40	chr2:231404200-231409200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr2:231404200-231409400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr2:231404200-231409600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr2:231404200-231410200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr2:231404400-231405600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:231404400-231406600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:231404400-231406600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr2:231404400-231408400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
48	chr2:231404400-231408400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:231404400-231409800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr2:231404400-231410000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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