Variant report

Variant	rs10492081
Chromosome Location	chr12:48474853-48474854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48355857..48357881-chr12:48473283..48476045,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134291	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1049392	0.86[YRI][hapmap]
rs10875733	0.81[ASW][hapmap];0.81[CHB][hapmap];0.86[YRI][hapmap]
rs11168373	0.81[CHB][hapmap]
rs11168404	0.81[ASW][hapmap];0.81[CHB][hapmap];0.85[YRI][hapmap]
rs11168424	0.82[YRI][hapmap]
rs12422355	0.81[CHB][hapmap];0.86[YRI][hapmap]
rs2286020	0.86[YRI][hapmap]
rs3742075	0.81[CHB][hapmap]
rs7302354	0.86[YRI][hapmap]
rs7303677	0.81[ASW][hapmap];0.81[CHB][hapmap];0.86[YRI][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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers 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	57 gene(s)	inside rSNPs	diseases
3	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer 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	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10492081	C12orf41	cis	parietal	SCAN
rs10492081	TMEM106C	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:48435200-48476200	Weak transcription	Stomach Mucosa	stomach
3	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:48441400-48482600	Weak transcription	Small Intestine	intestine
5	chr12:48443000-48478800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:48454000-48494000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:48454600-48478800	Weak transcription	Pancreas	Pancrea
9	chr12:48457400-48482000	Weak transcription	Right Ventricle	heart
10	chr12:48457600-48478600	Weak transcription	HSMMtube	muscle
11	chr12:48459200-48479000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:48463600-48476200	Weak transcription	HUVEC	blood vessel
13	chr12:48464400-48476200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:48464600-48489400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:48464800-48476000	Weak transcription	Fetal Brain Male	brain
16	chr12:48464800-48482400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:48465000-48477000	Weak transcription	Brain Angular Gyrus	brain
18	chr12:48465000-48478800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:48465000-48478800	Weak transcription	Aorta	Aorta
20	chr12:48465000-48487400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:48465800-48476800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:48466200-48481400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr12:48466800-48478800	Weak transcription	Esophagus	oesophagus
24	chr12:48468200-48476000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:48468200-48476000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:48468200-48476000	Weak transcription	HSMM	muscle
27	chr12:48468200-48478800	Weak transcription	HepG2	liver
28	chr12:48468400-48476000	Weak transcription	Fetal Lung	lung
29	chr12:48468400-48476200	Weak transcription	Brain Hippocampus Middle	brain
30	chr12:48468400-48476400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:48468400-48478600	Weak transcription	Colonic Mucosa	Colon
32	chr12:48468400-48478800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr12:48468400-48481400	Weak transcription	NHDF-Ad	bronchial
34	chr12:48468400-48482200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr12:48468400-48482200	Weak transcription	Brain Substantia Nigra	brain
36	chr12:48468600-48476000	Weak transcription	Fetal Kidney	kidney
37	chr12:48468600-48476800	Weak transcription	Brain Anterior Caudate	brain
38	chr12:48468600-48476800	Weak transcription	Colon Smooth Muscle	Colon
39	chr12:48468600-48498400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:48468800-48476800	Weak transcription	NHEK	skin
41	chr12:48468800-48477000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr12:48468800-48478800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:48468800-48482800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr12:48468800-48498200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr12:48470200-48497600	Weak transcription	Fetal Heart	heart
46	chr12:48470800-48492800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:48471400-48477400	Strong transcription	Primary B cells from peripheral blood	blood
48	chr12:48471400-48492000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:48471800-48477800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:48472000-48476000	Weak transcription	Primary B cells from cord blood	blood

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