Variant report

Variant	rs199738
Chromosome Location	chr6:25963456-25963457
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45196077..45196921-chr6:25962980..25963495,2	Hela-S3	cervix:
2	chr6:25962020..25964518-chr6:25991024..25993046,2	MCF-7	breast:
3	chr6:25961783..25964529-chr6:25992813..25995946,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200169	Chromatin interaction
ENSG00000272462	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10484431	1.00[JPT][hapmap]
rs10484434	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11751732	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11755492	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11757088	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11758372	1.00[CEU][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs11759668	1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs11964886	1.00[JPT][hapmap]
rs11969868	1.00[JPT][hapmap]
rs16891142	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17531978	1.00[JPT][hapmap]
rs17596719	1.00[JPT][hapmap]
rs185635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199728	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs199729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs199730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051538	1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2071302	1.00[JPT][hapmap]
rs2230654	1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2275906	1.00[JPT][hapmap]
rs2575170	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36125084	0.85[ASN][1000 genomes]
rs412968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59281021	0.85[ASN][1000 genomes]
rs62394537	0.95[EUR][1000 genomes]
rs626824	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6906460	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6925912	0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7746105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7757646	1.00[JPT][hapmap]
rs9689245	1.00[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	esv2755446	chr6:25924513-25981648	Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv432857	chr6:25957109-26072445	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	451 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs199738	ZNF193	cis	parietal	SCAN
rs199738	TRIM38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25962000-25964000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:25962000-25964400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:25962000-25964800	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr6:25962200-25964400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr6:25962200-25964400	Active TSS	Brain Anterior Caudate	brain
6	chr6:25962200-25964400	Active TSS	Brain Hippocampus Middle	brain
7	chr6:25962200-25964400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr6:25962200-25964800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:25962200-25965800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:25962400-25963800	Active TSS	Aorta	Aorta
11	chr6:25962400-25963800	Active TSS	Fetal Kidney	kidney
12	chr6:25962400-25964000	Active TSS	Gastric	stomach
13	chr6:25962400-25964200	Active TSS	Brain Angular Gyrus	brain
14	chr6:25962400-25964200	Active TSS	Brain Cingulate Gyrus	brain
15	chr6:25962400-25964200	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr6:25962400-25964200	Active TSS	Brain Substantia Nigra	brain
17	chr6:25962400-25964400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:25962400-25964400	Active TSS	Ovary	ovary
19	chr6:25962600-25963800	Active TSS	Primary T cells fromperipheralblood	blood
20	chr6:25962600-25963800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr6:25962600-25963800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:25962600-25963800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:25962600-25963800	Active TSS	Colon Smooth Muscle	Colon
24	chr6:25962600-25963800	Active TSS	Psoas Muscle	Psoas
25	chr6:25962600-25963800	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr6:25962600-25964000	Active TSS	Pancreas	Pancrea
27	chr6:25962600-25964200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:25962600-25964200	Active TSS	Duodenum Mucosa	Duodenum
29	chr6:25962600-25964200	Active TSS	Esophagus	oesophagus
30	chr6:25962600-25964200	Active TSS	Thymus	Thymus
31	chr6:25962600-25964400	Active TSS	Colonic Mucosa	Colon
32	chr6:25962600-25964400	Active TSS	Fetal Muscle Trunk	muscle
33	chr6:25962600-25964400	Active TSS	Left Ventricle	heart
34	chr6:25962600-25964400	Active TSS	Lung	lung
35	chr6:25962600-25964400	Active TSS	Right Ventricle	heart
36	chr6:25962600-25964600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr6:25962600-25964600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:25962600-25964600	Active TSS	Primary B cells from peripheral blood	blood
39	chr6:25962600-25964600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:25962600-25964600	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr6:25962600-25964600	Active TSS	NHLF	lung
42	chr6:25962600-25964800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:25962600-25964800	Active TSS	Right Atrium	heart
44	chr6:25962600-25964800	Active TSS	GM12878-XiMat	blood
45	chr6:25962600-25965000	Active TSS	HSMM	muscle
46	chr6:25962600-25965000	Active TSS	HSMMtube	muscle
47	chr6:25962600-25965200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:25962800-25963600	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr6:25962800-25963600	Active TSS	HMEC	breast
50	chr6:25962800-25963800	Active TSS	Breast Myoepithelial Primary Cells	Breast

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