Variant report

Variant	rs10506537
Chromosome Location	chr12:65030890-65030891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:65015218..65018137-chr12:65028300..65031254,2	K562	blood:
2	chr12:65023053..65026165-chr12:65027701..65030902,3	K562	blood:
3	chr12:65020670..65023700-chr12:65029685..65032659,3	MCF-7	breast:
4	chr12:65024701..65026859-chr12:65028365..65030970,2	MCF-7	breast:
5	chr12:65030293..65032004-chr12:65033712..65035363,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225195	Chromatin interaction
ENSG00000207546	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11175477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175479	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175480	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175482	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175485	0.87[LWK][hapmap]
rs11175486	0.87[LWK][hapmap]
rs11175492	0.88[ASW][hapmap];0.83[LWK][hapmap];0.85[YRI][hapmap]
rs11175495	0.87[AFR][1000 genomes]
rs12366918	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368329	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964094	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61931629	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832443	chr12:64878856-65057265	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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	15 gene(s)	inside rSNPs	diseases
5	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv438218	chr12:65017844-65037483	Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10506537	HMGA2	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65006800-65031800	Weak transcription	Dnd41	blood
2	chr12:65018600-65035000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:65019800-65047400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:65021200-65031200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr12:65021400-65043400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:65021800-65037000	Weak transcription	Adipose Nuclei	Adipose
7	chr12:65021800-65038000	Weak transcription	Ovary	ovary
8	chr12:65022400-65039600	Weak transcription	Osteobl	bone
9	chr12:65024000-65031200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:65024800-65031800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:65025000-65059600	Weak transcription	Thymus	Thymus
12	chr12:65025200-65044000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:65025800-65031400	Enhancers	HepG2	liver
14	chr12:65026400-65043200	Weak transcription	Fetal Stomach	stomach
15	chr12:65026800-65032400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:65027400-65032600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:65027400-65041800	Weak transcription	Spleen	Spleen
18	chr12:65027600-65031000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:65027600-65031800	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr12:65027600-65032600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:65027800-65031200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:65027800-65047600	Weak transcription	Psoas Muscle	Psoas
23	chr12:65028000-65032400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:65028000-65032600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:65028000-65036600	Weak transcription	Lung	lung
26	chr12:65028200-65047400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:65028400-65032000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:65028400-65032400	Weak transcription	Hela-S3	cervix
29	chr12:65028400-65037000	Weak transcription	HUVEC	blood vessel
30	chr12:65028400-65038600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:65028400-65047400	Weak transcription	NHDF-Ad	bronchial
32	chr12:65028400-65047400	Weak transcription	NHLF	lung
33	chr12:65028600-65056400	Weak transcription	NHEK	skin
34	chr12:65029000-65031200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:65029000-65041800	Weak transcription	Left Ventricle	heart
36	chr12:65029200-65031000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:65029200-65032800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:65029200-65039800	Enhancers	Primary T cells fromperipheralblood	blood
39	chr12:65029200-65041000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr12:65029200-65041600	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:65029400-65031800	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr12:65029400-65031800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr12:65029400-65032400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:65029400-65036800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:65029400-65038000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:65029600-65031200	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr12:65029600-65032400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:65029600-65032400	Weak transcription	K562	blood
49	chr12:65029600-65032600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:65029600-65036600	Weak transcription	Pancreas	Pancrea

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