Variant report

Variant	rs12368672
Chromosome Location	chr12:57512470-57512471
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57481437..57482964-chr12:57511233..57513007,2	K562	blood:
2	chr12:57508450..57511232-chr12:57511653..57513684,3	K562	blood:
3	chr12:57502941..57507087-chr12:57511781..57514626,3	K562	blood:
4	chr12:57398143..57400588-chr12:57512007..57514365,2	MCF-7	breast:
5	chr12:57510770..57512947-chr12:57552852..57554770,2	K562	blood:
6	chr12:57481437..57484038-chr12:57510875..57512733,2	K562	blood:

Variant related genes	Relation type
ENSG00000166886	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000166860	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10876963	0.81[ASN][1000 genomes]
rs11172106	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11172110	0.81[ASN][1000 genomes]
rs12298170	0.90[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12309413	0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs12312693	0.81[ASN][1000 genomes]
rs12322902	0.90[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs167769	1.00[ASW][hapmap];0.92[CEU][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]
rs3001425	0.95[EUR][1000 genomes]
rs3001427	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3122929	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs324011	1.00[ASW][hapmap];0.84[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs324013	0.82[GIH][hapmap]
rs3838958	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4759275	0.81[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap]
rs4759276	0.81[CHD][hapmap];0.88[GIH][hapmap]
rs73120411	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[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	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers 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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12368672	KIF5A	cis	cerebellum	SCAN
rs12368672	KRT2	cis	parietal	SCAN
rs12368672	STAT6	cis	multi-tissue	Pritchard
rs12368672	STAT6	cis	Frontal Cortex	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57505800-57521800	Weak transcription	Spleen	Spleen
2	chr12:57506200-57512600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:57506200-57520000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:57506200-57520400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:57506400-57512600	Weak transcription	Right Atrium	heart
6	chr12:57506600-57520400	Weak transcription	Stomach Mucosa	stomach
7	chr12:57506600-57520600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:57506600-57520600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:57506800-57512600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:57506800-57518200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:57506800-57519200	Weak transcription	Liver	Liver
12	chr12:57507200-57512600	Weak transcription	A549	lung
13	chr12:57511200-57513400	Weak transcription	K562	blood
14	chr12:57511600-57512600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:57511800-57512600	Weak transcription	HSMMtube	muscle
16	chr12:57511800-57513600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr12:57511800-57513600	Enhancers	HMEC	breast
18	chr12:57511800-57513800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:57511800-57513800	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr12:57511800-57513800	Enhancers	NHEK	skin
21	chr12:57512000-57513600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:57512000-57513600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:57512000-57513800	Enhancers	Primary B cells from cord blood	blood
24	chr12:57512200-57512800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr12:57512200-57513000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:57512200-57513400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:57512200-57513400	Enhancers	Primary B cells from peripheral blood	blood
28	chr12:57512200-57513400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:57512200-57513800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:57512200-57513800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr12:57512200-57513800	Enhancers	Hela-S3	cervix
32	chr12:57512200-57513800	Enhancers	HSMM	muscle
33	chr12:57512200-57513800	Enhancers	NHDF-Ad	bronchial
34	chr12:57512200-57513800	Enhancers	Osteobl	bone
35	chr12:57512400-57512800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:57512400-57512800	Enhancers	Placenta	Placenta
37	chr12:57512400-57512800	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr12:57512400-57512800	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr12:57512400-57513000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:57512400-57513000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:57512400-57513000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:57512400-57513000	Enhancers	Esophagus	oesophagus
43	chr12:57512400-57513000	Enhancers	GM12878-XiMat	blood
44	chr12:57512400-57513200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:57512400-57513200	Enhancers	Duodenum Mucosa	Duodenum
46	chr12:57512400-57513200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr12:57512400-57513200	Enhancers	Left Ventricle	heart
48	chr12:57512400-57513400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:57512400-57513400	Enhancers	Adipose Nuclei	Adipose
50	chr12:57512400-57513600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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