Variant report

Variant	rs11169747
Chromosome Location	chr12:51578953-51578954
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51577036..51579030-chr12:51592102..51594138,2	MCF-7	breast:
2	chr12:51474666..51478844-chr12:51578009..51583588,6	MCF-7	breast:
3	chr12:51577327..51580829-chr12:51630464..51634140,3	K562	blood:

Variant related genes	Relation type
ENSG00000183283	Chromatin interaction
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10876133	0.94[JPT][hapmap]
rs10876135	0.94[JPT][hapmap]
rs10876150	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169696	0.87[JPT][hapmap]
rs11169706	0.94[JPT][hapmap]
rs11169708	0.94[JPT][hapmap]
rs11169733	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169734	1.00[CEU][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169735	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169738	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11169740	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169741	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169751	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12230388	0.94[JPT][hapmap]
rs12424460	0.86[JPT][hapmap]
rs1493382	0.94[JPT][hapmap]
rs17125365	0.91[JPT][hapmap]
rs17125371	0.85[JPT][hapmap]
rs2359189	0.87[JPT][hapmap];0.90[YRI][hapmap]
rs2436636	0.94[JPT][hapmap]
rs2452794	0.94[JPT][hapmap]
rs2452795	0.93[JPT][hapmap]
rs2452796	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2640515	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2640518	1.00[CEU][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2640525	0.94[JPT][hapmap]
rs2640526	0.94[JPT][hapmap]
rs2730659	0.94[JPT][hapmap]
rs28392616	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2934092	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2956427	1.00[CEU][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768953	0.94[JPT][hapmap]
rs4768957	0.88[JPT][hapmap]
rs4768971	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6580802	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7136657	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7305956	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7309374	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7399089	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7399090	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7399214	0.94[JPT][hapmap]
rs7959264	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7964762	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7974242	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7980006	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8490	0.81[JPT][hapmap]

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	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11169747	IGFBP6	cis	parietal	SCAN
rs11169747	PFKM	cis	parietal	SCAN
rs11169747	AQP2	cis	cerebellum	SCAN
rs11169747	SMAGP	cis	parietal	SCAN
rs11169747	KRT76	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51567400-51583400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:51567400-51584000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:51567400-51610600	Weak transcription	Right Atrium	heart
4	chr12:51574800-51583400	Weak transcription	Aorta	Aorta
5	chr12:51575600-51583600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:51575800-51583600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:51576800-51580800	Enhancers	Fetal Muscle Leg	muscle
8	chr12:51577600-51582400	Weak transcription	Brain Substantia Nigra	brain
9	chr12:51577600-51583000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:51577800-51579600	Weak transcription	Fetal Thymus	thymus
11	chr12:51577800-51580200	Enhancers	HepG2	liver
12	chr12:51577800-51580600	Weak transcription	Fetal Stomach	stomach
13	chr12:51577800-51582000	Weak transcription	Brain Anterior Caudate	brain
14	chr12:51577800-51583400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:51578000-51580000	Weak transcription	GM12878-XiMat	blood
16	chr12:51578000-51580600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:51578000-51582200	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:51578000-51583000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:51578000-51583400	Weak transcription	Left Ventricle	heart
20	chr12:51578000-51583400	Weak transcription	Ovary	ovary
21	chr12:51578000-51583600	Weak transcription	Pancreas	Pancrea
22	chr12:51578000-51587600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:51578200-51579400	Enhancers	Fetal Muscle Trunk	muscle
24	chr12:51578200-51580200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:51578200-51580200	Enhancers	HSMMtube	muscle
26	chr12:51578200-51580200	Weak transcription	K562	blood
27	chr12:51578200-51580800	Weak transcription	Brain Angular Gyrus	brain
28	chr12:51578200-51581000	Weak transcription	Fetal Kidney	kidney
29	chr12:51578200-51582200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:51578200-51582200	Weak transcription	Brain Germinal Matrix	brain
31	chr12:51578200-51586000	Weak transcription	Fetal Heart	heart
32	chr12:51578200-51596800	Weak transcription	Fetal Lung	lung
33	chr12:51578400-51580000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:51578400-51580400	Weak transcription	Psoas Muscle	Psoas
35	chr12:51578400-51580800	Weak transcription	HSMM	muscle
36	chr12:51578400-51583800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:51578600-51580200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:51578800-51580200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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