Variant report

Variant	rs4367982
Chromosome Location	chr12:57531632-57531633
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57523914..57525971-chr12:57529903..57532518,2	K562	blood:
2	chr12:57530340..57532510-chr12:57555073..57556833,2	MCF-7	breast:
3	chr12:57531089..57533651-chr12:57579070..57581822,2	K562	blood:
4	chr12:57531018..57534803-chr12:57534919..57538004,3	MCF-7	breast:
5	chr12:57520649..57522697-chr12:57530721..57533381,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166888	Chromatin interaction
ENSG00000123384	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10747776	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10876964	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876965	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172113	0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.87[ASN][1000 genomes]
rs11172114	0.91[EUR][1000 genomes]
rs1385526	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1466535	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4257011	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4759044	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4759045	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4759277	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv559023	chr12:57530670-57616061	Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4367982	SUOX	cis	cerebellum	SCAN
rs4367982	SMARCC2	cis	cerebellum	SCAN
rs4367982	ATP5B	cis	cerebellum	SCAN
rs4367982	STAT6	cis	lymphoblastoid	seeQTL
rs4367982	KIF5A	cis	cerebellum	SCAN
rs4367982	SNORD59A	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57523400-57557200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:57523600-57532400	Weak transcription	Pancreas	Pancrea
3	chr12:57523800-57532600	Weak transcription	Gastric	stomach
4	chr12:57523800-57537000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr12:57524000-57542200	Weak transcription	HMEC	breast
6	chr12:57524000-57543000	Weak transcription	NHEK	skin
7	chr12:57525800-57531800	Weak transcription	Small Intestine	intestine
8	chr12:57525800-57534200	Genic enhancers	Primary monocytes fromperipheralblood	blood
9	chr12:57526200-57534800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:57526400-57532400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:57526600-57532200	Enhancers	Liver	Liver
12	chr12:57526600-57533400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:57527000-57532000	Weak transcription	Hela-S3	cervix
14	chr12:57527000-57534600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:57527200-57533400	Weak transcription	Fetal Kidney	kidney
16	chr12:57527800-57532000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:57528200-57531800	Weak transcription	Esophagus	oesophagus
18	chr12:57528800-57532200	Enhancers	Colonic Mucosa	Colon
19	chr12:57529000-57532400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:57529600-57532000	Weak transcription	A549	lung
21	chr12:57529800-57531800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:57529800-57531800	Enhancers	Brain Cingulate Gyrus	brain
23	chr12:57529800-57533000	Enhancers	Adipose Nuclei	Adipose
24	chr12:57529800-57533800	Genic enhancers	Fetal Intestine Small	intestine
25	chr12:57530000-57531800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:57530000-57531800	Weak transcription	Fetal Brain Female	brain
27	chr12:57530000-57532000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr12:57530000-57532200	Enhancers	Placenta	Placenta
29	chr12:57530000-57532600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:57530000-57537600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:57530200-57532200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:57530200-57532200	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr12:57530200-57533000	Genic enhancers	Fetal Stomach	stomach
34	chr12:57530400-57532000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr12:57530400-57532000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr12:57530400-57532200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:57530400-57532200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:57530400-57532200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:57530400-57532200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:57530400-57532200	Enhancers	Osteobl	bone
41	chr12:57530400-57532400	Weak transcription	Aorta	Aorta
42	chr12:57530400-57533400	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr12:57530400-57538200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:57530600-57531800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr12:57530600-57532000	Enhancers	Brain Anterior Caudate	brain
46	chr12:57530600-57532000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:57530600-57532000	Enhancers	HepG2	liver
48	chr12:57530600-57532200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr12:57530600-57532200	Weak transcription	Fetal Brain Male	brain
50	chr12:57530600-57532400	Enhancers	NHDF-Ad	bronchial

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