Variant report

Variant	rs12312593
Chromosome Location	chr12:104444199-104444200
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr12:104442977-104444428	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr12:104443003-104444354	SK-N-SH	brain:	n/a	n/a
3	KAP1	chr12:104443637-104444391	HEK293	kidney:	n/a	n/a
4	POLR2A	chr12:104443331-104444316	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:104443643-104444293	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr12:104444199-104444215	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104441752..104444274-chr12:104682358..104684016,2	K562	blood:
2	chr12:104359553..104362361-chr12:104443780..104446717,2	K562	blood:
3	chr12:104440302..104444353-chr12:104456677..104458918,3	K562	blood:
4	chr12:104441740..104444353-chr12:104456837..104458918,2	K562	blood:

No data

Variant related genes	Relation type
GLT8D2	TF binding region
ENSG00000111727	Chromatin interaction
ENSG00000120820	Chromatin interaction
ENSG00000139372	Chromatin interaction
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1047490	1.00[CHB][hapmap]
rs10861150	1.00[CHB][hapmap]
rs11111882	1.00[CHB][hapmap]
rs1165687	1.00[CHB][hapmap]
rs12312024	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314761	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319125	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368475	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369231	1.00[CHB][hapmap]
rs12372540	1.00[CHB][hapmap]
rs17805003	0.83[CEU][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs1866074	1.00[CHB][hapmap]
rs2629806	1.00[CHB][hapmap]
rs4135063	1.00[CHB][hapmap]
rs4135081	1.00[CHB][hapmap]
rs56090409	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539116	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs7132831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136550	1.00[CHB][hapmap]
rs7306515	1.00[CHB][hapmap]
rs73177963	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953041	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971994	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12312593	MMP7	trans	lymphoblastoid	seeQTL
rs12312593	GLT8D2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104441800-104444600	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr12:104442000-104444400	Active TSS	Aorta	Aorta
3	chr12:104442400-104444400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
4	chr12:104442400-104444600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:104442600-104444600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
6	chr12:104442600-104444600	Active TSS	Right Atrium	heart
7	chr12:104442800-104444200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:104442800-104444200	Active TSS	Colon Smooth Muscle	Colon
9	chr12:104442800-104444200	Active TSS	Stomach Smooth Muscle	stomach
10	chr12:104442800-104444400	Active TSS	Ovary	ovary
11	chr12:104442800-104444600	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr12:104442800-104444600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr12:104443000-104444200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr12:104443000-104444200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:104443000-104444200	Active TSS	Fetal Lung	lung
16	chr12:104443000-104444400	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr12:104443000-104444600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:104443000-104444600	Active TSS	NHDF-Ad	bronchial
19	chr12:104443200-104444200	Active TSS	H9 Cell Line	embryonic stem cell
20	chr12:104443200-104444200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr12:104443200-104444200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr12:104443200-104444200	Bivalent/Poised TSS	Fetal Brain Male	brain
23	chr12:104443200-104444200	Active TSS	Fetal Kidney	kidney
24	chr12:104443200-104444400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:104443200-104444400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
26	chr12:104443200-104444600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
27	chr12:104443400-104444200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:104443400-104444200	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:104443400-104444200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:104443400-104444200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:104443400-104444200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:104443400-104444200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:104443400-104444200	Active TSS	Left Ventricle	heart
34	chr12:104443400-104444400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:104443400-104444400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:104443400-104444400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
37	chr12:104443400-104444400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:104443400-104444400	Bivalent/Poised TSS	Colonic Mucosa	Colon
39	chr12:104443400-104444400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
40	chr12:104443400-104444400	Flanking Active TSS	Placenta	Placenta
41	chr12:104443400-104444400	Active TSS	Psoas Muscle	Psoas
42	chr12:104443400-104444400	Active TSS	Right Ventricle	heart
43	chr12:104443400-104444400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
44	chr12:104443400-104444400	Flanking Active TSS	NHEK	skin
45	chr12:104443400-104444600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:104443600-104444200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:104443600-104444200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
48	chr12:104443600-104444200	Bivalent Enhancer	Primary B cells from cord blood	blood
49	chr12:104443600-104444200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
50	chr12:104443600-104444200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood

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