Variant report

Variant	rs3014996
Chromosome Location	chr12:68313156-68313157
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:68307323..68311643-chr12:68312148..68315840,4	K562	blood:
2	chr12:68306230..68308010-chr12:68310665..68313391,3	MCF-7	breast:
3	chr12:68302716..68305733-chr12:68312803..68316283,4	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11176930	0.86[ASN][1000 genomes]
rs1905454	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1922656	0.86[EUR][1000 genomes]
rs2077121	0.87[EUR][1000 genomes]
rs2192783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192784	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2930116	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3015000	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3850591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs734542	0.86[EUR][1000 genomes]
rs741290	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3411149	chr12:68066948-68435533	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1039638	chr12:68293351-68399871	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv899219	chr12:68293419-68353649	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1047675	chr12:68303674-68337325	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3014996	HMGA2	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:68307600-68318800	Weak transcription	Fetal Heart	heart
2	chr12:68310000-68317600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:68310400-68313400	Weak transcription	Stomach Mucosa	stomach
4	chr12:68310400-68319000	Weak transcription	Left Ventricle	heart
5	chr12:68310600-68313200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:68310600-68313200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:68310600-68313600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:68310600-68313800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:68310600-68317000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:68310600-68317400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:68310600-68318200	Weak transcription	Fetal Muscle Leg	muscle
12	chr12:68310600-68329800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:68310800-68313400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:68310800-68313800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:68310800-68313800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:68310800-68313800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr12:68310800-68313800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:68310800-68313800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:68311000-68313400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:68311200-68313600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:68311400-68314000	Enhancers	NHDF-Ad	bronchial
22	chr12:68312000-68317000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:68312200-68315000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:68312200-68315800	Enhancers	HSMMtube	muscle
25	chr12:68312400-68313800	Enhancers	HMEC	breast
26	chr12:68312400-68316200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:68312800-68313800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:68312800-68314000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:68312800-68315200	Enhancers	NH-A	brain
30	chr12:68313000-68313400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:68313000-68313400	Flanking Active TSS	NHEK	skin
32	chr12:68313000-68314000	Enhancers	A549	lung
33	chr12:68313000-68314600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:68313000-68314600	Enhancers	HSMM	muscle
35	chr12:68313000-68315000	Enhancers	Muscle Satellite Cultured Cells	--
36	chr12:68313000-68315200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:68313000-68316000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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