Variant report

Variant	rs7971994
Chromosome Location	chr12:104440421-104440422
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104438711..104441073-chr12:104451682..104453689,2	K562	blood:
2	chr12:104438680..104440536-chr12:104458293..104460022,2	MCF-7	breast:
3	chr12:104440302..104444353-chr12:104456677..104458918,3	K562	blood:

Variant related genes	Relation type
ENSG00000120820	Chromatin interaction
ENSG00000111727	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];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12312593	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]
rs12314761	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319125	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368475	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.87[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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539116	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap]
rs7132831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][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]
rs7136550	1.00[CHB][hapmap]
rs7306515	1.00[CHB][hapmap]
rs73177963	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];1.00[AMR][1000 genomes];1.00[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
rs7971994	GLT8D2	cis	Adipose Subcutaneous	GTEx
rs7971994	MMP7	trans	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104408800-104442200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:104435000-104442000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:104435800-104441600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:104437600-104442000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr12:104438000-104440600	Weak transcription	Fetal Brain Female	brain
6	chr12:104438400-104441800	Enhancers	Colon Smooth Muscle	Colon
7	chr12:104438800-104440600	Enhancers	Fetal Heart	heart
8	chr12:104438800-104440800	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr12:104439200-104442000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr12:104439400-104440600	Enhancers	Stomach Smooth Muscle	stomach
11	chr12:104439400-104441200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:104439400-104442000	Weak transcription	Adipose Nuclei	Adipose
13	chr12:104439400-104442200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr12:104439400-104442600	Weak transcription	Right Atrium	heart
15	chr12:104439400-104443400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:104439400-104443400	Weak transcription	Left Ventricle	heart
17	chr12:104439400-104443400	Weak transcription	Lung	lung
18	chr12:104439400-104443400	Weak transcription	Right Ventricle	heart
19	chr12:104439400-104443800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:104439600-104440800	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:104439600-104441800	Weak transcription	HMEC	breast
22	chr12:104439600-104442000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:104439600-104442200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:104439600-104442400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:104439600-104442400	Weak transcription	Fetal Stomach	stomach
26	chr12:104439600-104442400	Weak transcription	HSMM	muscle
27	chr12:104439600-104442400	Weak transcription	HSMMtube	muscle
28	chr12:104439600-104443400	Weak transcription	Psoas Muscle	Psoas
29	chr12:104440000-104442400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:104440000-104443400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:104440200-104441000	Enhancers	Aorta	Aorta
32	chr12:104440200-104441600	Enhancers	Ovary	ovary
33	chr12:104440200-104443000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:104440200-104443200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:104440400-104441400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr12:104440400-104441800	Weak transcription	Fetal Lung	lung

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