Variant report

Variant	rs6728193
Chromosome Location	chr2:231406332-231406333
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 5 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10202660	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288668	0.87[CHD][hapmap];0.81[JPT][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6728193	TIGD1	cis	cerebellum	SCAN
rs6728193	SNORD82	cis	cerebellum	SCAN
rs6728193	UGT1A1	cis	cerebellum	SCAN

Chromatin state (count:70 , 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	chr2:231390800-231409200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:231391000-231406400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:231401000-231430200	Weak transcription	Pancreas	Pancrea
6	chr2:231401400-231408600	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:231401800-231406400	Weak transcription	Osteobl	bone
8	chr2:231401800-231409200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:231403200-231406600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:231403200-231410200	Strong transcription	Primary B cells from cord blood	blood
11	chr2:231403600-231407800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:231403600-231408600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:231403800-231406800	Strong transcription	Ovary	ovary
14	chr2:231403800-231408800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr2:231403800-231409600	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr2:231404000-231406800	ZNF genes & repeats	Aorta	Aorta
17	chr2:231404000-231406800	Strong transcription	Spleen	Spleen
18	chr2:231404000-231407200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:231404000-231407200	Strong transcription	Left Ventricle	heart
20	chr2:231404000-231408400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:231404000-231409000	Strong transcription	Primary T cells from cord blood	blood
22	chr2:231404000-231409000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr2:231404000-231417200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:231404200-231406400	Genic enhancers	GM12878-XiMat	blood
25	chr2:231404200-231409000	Strong transcription	Adipose Nuclei	Adipose
26	chr2:231404200-231409200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:231404200-231409400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:231404200-231409600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:231404200-231410200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr2:231404400-231406600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:231404400-231406600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:231404400-231408400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
33	chr2:231404400-231408400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:231404400-231409800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr2:231404400-231410000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:231404600-231409000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr2:231404600-231416400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:231404800-231408800	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:231404800-231410800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr2:231405000-231409800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:231405200-231406800	Strong transcription	Fetal Muscle Leg	muscle
42	chr2:231405200-231407200	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr2:231405200-231407600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:231405200-231408800	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr2:231405400-231409800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:231405400-231411600	Weak transcription	Placenta	Placenta
47	chr2:231405400-231411800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:231405600-231406400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:231405600-231406400	Strong transcription	Thymus	Thymus
50	chr2:231405600-231406800	Strong transcription	Lung	lung

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