Variant report

Variant	rs2041769
Chromosome Location	chr12:68310484-68310485
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:68304416..68306533-chr12:68307789..68310636,2	MCF-7	breast:
2	chr12:68307323..68311643-chr12:68312148..68315840,4	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10878695	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10878696	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10878697	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176936	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11176937	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1351768	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1905453	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2160243	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2160244	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2192784	0.91[CEU][hapmap]
rs2192785	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2216012	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2904502	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2908764	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2930118	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2930120	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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
rs2041769	HMGA2	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:68305600-68312400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:68305600-68312400	Weak transcription	HMEC	breast
3	chr12:68305600-68313000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:68305800-68311400	Weak transcription	NHDF-Ad	bronchial
5	chr12:68305800-68312600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:68307600-68318800	Weak transcription	Fetal Heart	heart
7	chr12:68309400-68311000	Enhancers	NHEK	skin
8	chr12:68309600-68310800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:68309800-68310600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr12:68309800-68310800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr12:68309800-68310800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr12:68309800-68310800	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr12:68309800-68311000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr12:68309800-68311200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr12:68310000-68310600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr12:68310000-68310600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr12:68310000-68310600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr12:68310000-68310600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:68310000-68310600	Enhancers	Fetal Muscle Leg	muscle
20	chr12:68310000-68310600	Enhancers	Psoas Muscle	Psoas
21	chr12:68310000-68310800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr12:68310000-68317600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:68310200-68310600	Enhancers	H9 Cell Line	embryonic stem cell
24	chr12:68310200-68310600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:68310200-68310800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:68310200-68310800	Enhancers	HSMM	muscle
27	chr12:68310200-68310800	Enhancers	HSMMtube	muscle
28	chr12:68310200-68312000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:68310400-68312000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:68310400-68312200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:68310400-68313000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:68310400-68313400	Weak transcription	Stomach Mucosa	stomach
33	chr12:68310400-68319000	Weak transcription	Left Ventricle	heart

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