Variant report

Variant	rs10878098
Chromosome Location	chr12:64352091-64352092
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:64350699..64353399-chr12:64355633..64359154,3	K562	blood:
2	chr12:64239389..64242178-chr12:64352043..64353568,2	MCF-7	breast:

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs10878096	0.81[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv559201	chr12:64333212-64366408	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10878098	HMGA2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64312400-64385000	Weak transcription	Aorta	Aorta
2	chr12:64328800-64360800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:64340000-64360200	Weak transcription	NHEK	skin
4	chr12:64344200-64361000	Weak transcription	HMEC	breast
5	chr12:64344600-64352400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr12:64344600-64359800	Weak transcription	Small Intestine	intestine
7	chr12:64344600-64363800	Weak transcription	Fetal Intestine Small	intestine
8	chr12:64345400-64363800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:64346000-64365400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:64347000-64355000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:64347000-64361400	Weak transcription	Brain Anterior Caudate	brain
12	chr12:64347200-64352200	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:64348600-64354400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:64349200-64355200	Enhancers	Fetal Brain Male	brain
15	chr12:64350000-64354600	Enhancers	Fetal Brain Female	brain
16	chr12:64350000-64354600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:64350000-64354800	Weak transcription	Osteobl	bone
18	chr12:64350200-64354600	Weak transcription	Right Atrium	heart
19	chr12:64350200-64355000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:64350200-64355000	Weak transcription	Lung	lung
21	chr12:64350200-64356800	Weak transcription	A549	lung
22	chr12:64350400-64352200	Weak transcription	Fetal Kidney	kidney
23	chr12:64350400-64355000	Weak transcription	Ovary	ovary
24	chr12:64350400-64361000	Weak transcription	HSMM	muscle
25	chr12:64350600-64355200	Weak transcription	Adipose Nuclei	Adipose
26	chr12:64350600-64357200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr12:64351000-64352200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:64351000-64352200	Enhancers	Pancreas	Pancrea
29	chr12:64351200-64352400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:64351200-64355000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:64351200-64355000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:64351200-64355000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:64351200-64357000	Weak transcription	Brain Substantia Nigra	brain
34	chr12:64351400-64352200	Strong transcription	NHLF	lung
35	chr12:64352000-64352200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:64352000-64353800	Weak transcription	NHDF-Ad	bronchial

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