Variant report

Variant	rs11168363
Chromosome Location	chr12:48420713-48420714
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	chr12:48420267..48422081-chr12:48425006..48427209,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10492082	0.98[ASN][1000 genomes]
rs1049392	0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs10747529	1.00[JPT][hapmap]
rs10875726	0.92[ASN][1000 genomes]
rs10875727	0.92[ASN][1000 genomes]
rs10875733	0.81[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[ASN][1000 genomes]
rs10875739	0.96[CHD][hapmap];1.00[JPT][hapmap]
rs10875752	0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs10875754	1.00[JPT][hapmap]
rs10875761	0.81[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs10875766	1.00[JPT][hapmap]
rs11168350	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs11168353	0.90[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168354	0.90[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168358	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11168361	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168373	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11168378	0.81[ASN][1000 genomes]
rs11168404	0.81[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs11168417	0.81[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs11168424	0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs11168434	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs11168435	0.81[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs11168438	1.00[JPT][hapmap]
rs11168445	1.00[JPT][hapmap]
rs11168448	0.96[GIH][hapmap];1.00[JPT][hapmap]
rs11168453	0.96[GIH][hapmap];1.00[JPT][hapmap]
rs11168454	1.00[JPT][hapmap]
rs11834818	0.84[ASN][1000 genomes]
rs12228924	0.81[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]
rs12422355	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12423250	0.94[JPT][hapmap]
rs12426981	0.84[ASN][1000 genomes]
rs17122567	0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1859440	0.91[ASN][1000 genomes]
rs1859442	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1859443	0.94[JPT][hapmap]
rs1978161	0.96[CHD][hapmap];0.82[JPT][hapmap]
rs2056448	0.96[ASN][1000 genomes]
rs2240306	0.94[ASN][1000 genomes]
rs2286020	0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs2408954	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3742075	0.89[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs3825403	0.95[CHD][hapmap];1.00[JPT][hapmap]
rs4258439	0.91[CHD][hapmap];1.00[JPT][hapmap]
rs58086963	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59667534	0.98[ASN][1000 genomes]
rs6580658	0.80[JPT][hapmap]
rs7135261	0.87[EUR][1000 genomes]
rs7299704	0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7302354	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs7303677	0.81[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs733592	0.91[ASN][1000 genomes]
rs7484942	0.96[GIH][hapmap];1.00[JPT][hapmap]
rs765260	0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7962390	0.96[GIH][hapmap];1.00[JPT][hapmap]
rs7962569	0.96[GIH][hapmap];0.94[JPT][hapmap]
rs8181670	0.81[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs886589	0.96[CHD][hapmap];1.00[JPT][hapmap]
rs954326	0.94[JPT][hapmap]
rs9651981	0.81[CEU][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9804751	0.96[GIH][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11168363	TMEM106C	cis	parietal	SCAN
rs11168363	C12orf41	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48416800-48423400	Weak transcription	Right Atrium	heart
2	chr12:48417600-48420800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:48417800-48421400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:48417800-48423400	Weak transcription	Fetal Lung	lung
5	chr12:48418000-48422200	Weak transcription	Fetal Heart	heart
6	chr12:48418200-48422200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr12:48418200-48424200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:48418400-48425800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:48418600-48421000	Enhancers	Fetal Intestine Small	intestine
10	chr12:48418600-48425200	Enhancers	Fetal Intestine Large	intestine
11	chr12:48418800-48421000	Weak transcription	Right Ventricle	heart
12	chr12:48419200-48422400	Weak transcription	K562	blood
13	chr12:48419600-48421000	Enhancers	HepG2	liver
14	chr12:48419800-48421400	Enhancers	Fetal Thymus	thymus
15	chr12:48420000-48422400	Weak transcription	Colon Smooth Muscle	Colon
16	chr12:48420000-48424200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:48420200-48422800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:48420200-48423800	Enhancers	Primary hematopoietic stem cells	blood
19	chr12:48420200-48424200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:48420400-48421000	Enhancers	Fetal Kidney	kidney
21	chr12:48420400-48421800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr12:48420400-48424000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:48420400-48424000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:48420400-48424200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:48420400-48429000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:48420600-48422200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:48420600-48424200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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