Variant report

Variant	rs11168370
Chromosome Location	chr12:48435280-48435281
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48433439..48436867-chr12:48436934..48440362,3	K562	blood:
2	chr12:48422677..48425414-chr12:48434042..48436175,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10875724	0.80[EUR][1000 genomes]
rs10875725	0.82[GIH][hapmap]
rs10875728	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10875729	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10875730	0.96[EUR][1000 genomes]
rs10875731	0.98[EUR][1000 genomes]
rs10875732	0.92[CEU][hapmap];0.97[EUR][1000 genomes]
rs10875735	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10875737	0.80[EUR][1000 genomes]
rs10875738	0.82[EUR][1000 genomes]
rs10875740	0.82[EUR][1000 genomes]
rs10875746	0.82[GIH][hapmap];0.85[TSI][hapmap]
rs10875747	0.81[EUR][1000 genomes]
rs10875748	0.81[EUR][1000 genomes]
rs10875750	0.86[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap]
rs11168355	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs11168357	0.85[GIH][hapmap];0.85[TSI][hapmap]
rs11168369	0.86[CEU][hapmap];0.98[EUR][1000 genomes]
rs11168371	0.93[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs11168374	0.98[EUR][1000 genomes]
rs11168383	0.82[EUR][1000 genomes]
rs11168386	0.82[EUR][1000 genomes]
rs11168401	0.82[EUR][1000 genomes]
rs11168403	0.85[CEU][hapmap]
rs11168414	0.86[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs11168418	0.86[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs11168420	0.86[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs11168425	0.82[GIH][hapmap]
rs11168427	0.86[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap]
rs11168433	0.86[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap]
rs12296244	0.98[EUR][1000 genomes]
rs12297004	0.83[EUR][1000 genomes]
rs12297470	0.82[GIH][hapmap]
rs12301339	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs12304476	0.93[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs12305182	0.80[EUR][1000 genomes]
rs12305511	0.80[CEU][hapmap];0.94[TSI][hapmap]
rs12306451	0.93[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs12310813	0.82[GIH][hapmap]
rs12310999	0.98[EUR][1000 genomes]
rs12311953	0.80[EUR][1000 genomes]
rs12313300	0.82[EUR][1000 genomes]
rs12313404	0.81[EUR][1000 genomes]
rs12315625	0.80[EUR][1000 genomes]
rs17122620	0.82[EUR][1000 genomes]
rs17122666	0.86[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs1859445	0.84[GIH][hapmap]
rs2158516	0.82[EUR][1000 genomes]
rs2228500	0.86[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs2269935	0.86[CEU][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs2269936	0.85[CEU][hapmap];0.96[EUR][1000 genomes]
rs2286021	0.81[EUR][1000 genomes]
rs3782910	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs3782911	0.82[EUR][1000 genomes]
rs4760609	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs4760622	0.80[CEU][hapmap];0.94[TSI][hapmap]
rs4760676	0.80[EUR][1000 genomes]
rs4760680	0.82[EUR][1000 genomes]
rs4760681	0.86[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs4760687	0.82[GIH][hapmap]
rs4760695	0.80[CEU][hapmap];0.94[TSI][hapmap]
rs58952582	0.82[EUR][1000 genomes]
rs60761335	0.82[EUR][1000 genomes]
rs61918774	0.98[EUR][1000 genomes]
rs61918806	0.81[EUR][1000 genomes]
rs61918809	0.80[EUR][1000 genomes]
rs61918810	0.82[EUR][1000 genomes]
rs725454	0.86[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs73102065	0.82[EUR][1000 genomes]
rs8804	0.86[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap]
rs886588	0.93[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs989144	0.93[CEU][hapmap];0.82[EUR][1000 genomes]

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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11168370	LOC255411	cis	cerebellum	SCAN
rs11168370	SENP1	cis	cerebellum	SCAN
rs11168370	RP1-228P16.1	cis	Thyroid	GTEx
rs11168370	PRKAG1	cis	parietal	SCAN
rs11168370	ASB8	cis	cerebellum	SCAN
rs11168370	LMBR1L	cis	cerebellum	SCAN
rs11168370	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs11168370	SENP1	cis	parietal	SCAN
rs11168370	RP1-228P16.1	cis	Artery Tibial	GTEx
rs11168370	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11168370	AQP6	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48422800-48438800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:48424800-48437400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr12:48427600-48435600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:48429200-48437000	Weak transcription	GM12878-XiMat	blood
5	chr12:48429400-48435400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:48429600-48436400	Weak transcription	HMEC	breast
7	chr12:48431400-48436600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr12:48431400-48438200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:48431400-48438400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:48431600-48437800	Weak transcription	Brain Germinal Matrix	brain
11	chr12:48431800-48435600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:48431800-48435800	Weak transcription	Primary B cells from cord blood	blood
13	chr12:48431800-48436000	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:48431800-48436400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr12:48431800-48436400	Weak transcription	Placenta	Placenta
16	chr12:48431800-48437000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr12:48431800-48437000	Weak transcription	Liver	Liver
18	chr12:48431800-48437600	Weak transcription	Adipose Nuclei	Adipose
19	chr12:48431800-48438200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:48431800-48438200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:48431800-48438200	Weak transcription	Fetal Stomach	stomach
22	chr12:48431800-48438200	Weak transcription	Lung	lung
23	chr12:48431800-48438200	Weak transcription	Pancreas	Pancrea
24	chr12:48431800-48438400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:48431800-48438400	Weak transcription	K562	blood
26	chr12:48431800-48438800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:48431800-48456600	Weak transcription	NHLF	lung
28	chr12:48432000-48435800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr12:48432000-48436000	Weak transcription	Fetal Thymus	thymus
30	chr12:48432000-48436400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:48432000-48436400	Weak transcription	Brain Angular Gyrus	brain
32	chr12:48432000-48436400	Weak transcription	Fetal Lung	lung
33	chr12:48432000-48436400	Weak transcription	HSMM	muscle
34	chr12:48432000-48436800	Weak transcription	NH-A	brain
35	chr12:48432000-48437000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr12:48432000-48438200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:48432000-48438200	Weak transcription	Right Ventricle	heart
38	chr12:48432000-48438200	Weak transcription	Spleen	Spleen
39	chr12:48432000-48438400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:48432000-48438400	Weak transcription	Fetal Kidney	kidney
41	chr12:48432000-48438400	Weak transcription	Ovary	ovary
42	chr12:48432000-48438800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr12:48432000-48438800	Weak transcription	NHDF-Ad	bronchial
44	chr12:48432000-48439800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr12:48432000-48439800	Weak transcription	Fetal Heart	heart
46	chr12:48432000-48463400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr12:48432200-48435600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr12:48432200-48436200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:48432200-48436400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:48432200-48436600	Weak transcription	Primary monocytes fromperipheralblood	blood

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