Variant report

Variant	rs12722498
Chromosome Location	chr10:6095836-6095837
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12722491	0.80[EUR][1000 genomes]
rs12722492	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12722494	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12722503	0.91[AMR][1000 genomes]
rs12722528	0.91[AMR][1000 genomes]
rs17421433	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1924137	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228149	0.80[AMR][1000 genomes]
rs2245675	0.82[CHB][hapmap]
rs2256774	0.82[CHB][hapmap]
rs2274037	1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs41294685	0.80[AMR][1000 genomes]
rs41294927	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41294935	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41295051	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62626316	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62626324	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72776071	0.82[AMR][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	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv894814	chr10:6078032-6100725	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12722498	MED13L	trans	lymphoblastoid	seeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6093400-6096000	Weak transcription	Hela-S3	cervix
2	chr10:6093400-6096200	Enhancers	Primary hematopoietic stem cells	blood
3	chr10:6093400-6096200	Enhancers	Rectal Mucosa Donor 29	rectum
4	chr10:6093400-6096400	Enhancers	Fetal Thymus	thymus
5	chr10:6093400-6096800	Enhancers	Adipose Nuclei	Adipose
6	chr10:6093400-6097200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr10:6093400-6101000	Weak transcription	Psoas Muscle	Psoas
8	chr10:6093400-6102800	Enhancers	Primary B cells from peripheral blood	blood
9	chr10:6093800-6104200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
10	chr10:6094000-6096000	Enhancers	HMEC	breast
11	chr10:6094000-6097400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
12	chr10:6094200-6096400	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr10:6094200-6097200	Enhancers	Spleen	Spleen
14	chr10:6094400-6096200	Enhancers	Placenta	Placenta
15	chr10:6094400-6096200	Enhancers	Small Intestine	intestine
16	chr10:6094600-6096000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr10:6094600-6096600	Enhancers	Primary B cells from cord blood	blood
18	chr10:6094800-6096000	Enhancers	Thymus	Thymus
19	chr10:6094800-6096400	Enhancers	Primary T cells from cord blood	blood
20	chr10:6094800-6096400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr10:6094800-6096400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr10:6094800-6096800	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr10:6094800-6097200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr10:6095000-6096200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr10:6095000-6096200	Enhancers	HUVEC	blood vessel
26	chr10:6095000-6096400	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr10:6095000-6096400	Enhancers	Gastric	stomach
28	chr10:6095000-6096800	Enhancers	Fetal Intestine Small	intestine
29	chr10:6095000-6097000	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr10:6095000-6097200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr10:6095200-6096000	Weak transcription	Lung	lung
32	chr10:6095200-6096000	Weak transcription	Right Atrium	heart
33	chr10:6095200-6096200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr10:6095200-6096400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr10:6095200-6096600	Enhancers	Primary T cells fromperipheralblood	blood
36	chr10:6095200-6096600	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr10:6095200-6098400	Weak transcription	Left Ventricle	heart
38	chr10:6095400-6096000	Enhancers	Liver	Liver
39	chr10:6095400-6097400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr10:6095600-6096200	Enhancers	Colonic Mucosa	Colon
41	chr10:6095600-6096400	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr10:6095800-6096000	Flanking Active TSS	GM12878-XiMat	blood
43	chr10:6095800-6096000	Enhancers	K562	blood
44	chr10:6095800-6096200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr10:6095800-6096200	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr10:6095800-6096200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr10:6095800-6096200	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr10:6095800-6096200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr10:6095800-6096200	Flanking Active TSS	Stomach Mucosa	stomach
50	chr10:6095800-6096200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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