Variant report

Variant	rs662138
Chromosome Location	chr6:160564476-160564477
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:160562545..160565389-chr6:160568251..160570713,2	K562	blood:
2	chr6:160558415..160560977-chr6:160562640..160565543,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10945664	1.00[ASN][1000 genomes]
rs11753995	0.90[CEU][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1564348	0.90[CEU][hapmap];0.82[MEX][hapmap]
rs45584532	1.00[ASN][1000 genomes]
rs456598	0.90[GIH][hapmap]
rs56384560	1.00[ASN][1000 genomes]
rs62440901	0.81[EUR][1000 genomes]
rs6937722	1.00[ASN][1000 genomes]
rs73025542	1.00[ASN][1000 genomes]
rs7762846	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758089	chr6:160372244-161234665	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2759484	chr6:160372244-161234665	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv35098	chr6:160422589-161070870	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2757197	chr6:160432331-161070870	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv818463	chr6:160435569-161025547	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv533582	chr6:160554084-160579554	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Blood metabolite levels	24816252	GWAS catalog
Metabolic traits	21886157	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs662138	GTF2H5	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:160539400-160580400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:160539600-160574600	Weak transcription	Adipose Nuclei	Adipose
3	chr6:160540200-160576200	Weak transcription	Right Ventricle	heart
4	chr6:160540400-160568800	Weak transcription	Esophagus	oesophagus
5	chr6:160554800-160582800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:160559000-160573000	Weak transcription	Left Ventricle	heart
7	chr6:160559200-160564600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:160559200-160581600	Weak transcription	Gastric	stomach
9	chr6:160559200-160581600	Weak transcription	Pancreas	Pancrea
10	chr6:160559600-160577400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:160559800-160566000	Weak transcription	Brain Angular Gyrus	brain
12	chr6:160559800-160573800	Weak transcription	Fetal Intestine Small	intestine
13	chr6:160559800-160581600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:160560200-160580600	Weak transcription	Fetal Intestine Large	intestine
15	chr6:160560200-160581800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:160560400-160584600	Weak transcription	Spleen	Spleen
17	chr6:160560600-160567600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:160560800-160570800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:160560800-160583000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:160561000-160575000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:160562200-160567600	Weak transcription	Ovary	ovary
22	chr6:160562200-160567600	Weak transcription	Psoas Muscle	Psoas
23	chr6:160562400-160583600	Weak transcription	HSMMtube	muscle
24	chr6:160562800-160567000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:160563000-160564800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:160563000-160581000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:160563200-160567600	Weak transcription	Osteobl	bone
28	chr6:160563400-160566800	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:160563400-160574000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:160563400-160581600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:160563400-160581800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:160563600-160567600	Weak transcription	Aorta	Aorta
33	chr6:160563600-160567800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:160563600-160580200	Strong transcription	Liver	Liver
35	chr6:160563800-160565600	Strong transcription	Fetal Muscle Leg	muscle
36	chr6:160563800-160567600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:160564000-160567200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr6:160564200-160565400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:160564400-160565200	Strong transcription	Skeletal Muscle Female	skeletal muscle

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