Variant report

Variant	rs11060853
Chromosome Location	chr12:123424071-123424072
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	chr12:123415535..123420026-chr12:123422545..123426280,4	K562	blood:
2	chr12:123413568..123415277-chr12:123423150..123425253,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10773921	0.95[JPT][hapmap]
rs10848428	0.81[JPT][hapmap]
rs11608811	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs11609798	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12425009	0.82[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12425850	0.83[ASN][1000 genomes]
rs1727307	0.81[JPT][hapmap]
rs1790094	0.81[JPT][hapmap]
rs1790106	0.81[JPT][hapmap]
rs1790121	0.81[JPT][hapmap]
rs28755851	0.83[ASN][1000 genomes]
rs3741530	0.82[ASN][1000 genomes]
rs3759115	0.82[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3897102	0.84[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4148863	0.81[JPT][hapmap]
rs4148866	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4275659	0.82[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs61955196	0.88[ASN][1000 genomes]
rs61955214	0.82[ASN][1000 genomes]
rs7135296	0.84[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7296418	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7305511	0.82[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7957096	0.90[JPT][hapmap]
rs883562	0.84[ASN][1000 genomes]
rs884956	0.84[ASN][1000 genomes]
rs949143	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv976725	chr12:123412328-123429898	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11060853	C12orf65	cis	cerebellum	SCAN
rs11060853	HIP1R	cis	parietal	SCAN
rs11060853	CDK2AP1	cis	cerebellum	SCAN
rs11060853	TMEM120B	cis	parietal	SCAN
rs11060853	MGC7036	Cis_1M	lymphoblastoid	RTeQTL
rs11060853	DDX55	cis	parietal	SCAN
rs11060853	IL31	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123401400-123425200	Weak transcription	Esophagus	oesophagus
2	chr12:123401400-123426000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:123402600-123429200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:123402800-123426600	Weak transcription	NHLF	lung
5	chr12:123402800-123429200	Weak transcription	Gastric	stomach
6	chr12:123402800-123430800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:123403000-123426400	Weak transcription	Left Ventricle	heart
8	chr12:123403000-123428800	Weak transcription	Lung	lung
9	chr12:123403000-123444200	Weak transcription	Aorta	Aorta
10	chr12:123403400-123427000	Weak transcription	A549	lung
11	chr12:123405200-123424800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:123405200-123428600	Weak transcription	NHEK	skin
13	chr12:123406800-123426600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr12:123409400-123427600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:123411800-123428800	Weak transcription	Fetal Brain Male	brain
16	chr12:123412400-123427200	Weak transcription	Adipose Nuclei	Adipose
17	chr12:123412800-123427400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:123412800-123431800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:123412800-123449200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:123413200-123424400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:123413400-123425400	Strong transcription	Fetal Brain Female	brain
22	chr12:123413400-123427200	Weak transcription	Small Intestine	intestine
23	chr12:123413400-123427400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:123413400-123427600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr12:123413400-123427600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:123413400-123449600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr12:123413600-123431400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:123413600-123450000	Weak transcription	Primary T cells from cord blood	blood
29	chr12:123414000-123432400	Weak transcription	Fetal Kidney	kidney
30	chr12:123414800-123427400	Weak transcription	Spleen	Spleen
31	chr12:123414800-123427800	Weak transcription	Right Ventricle	heart
32	chr12:123415600-123429000	Weak transcription	Pancreas	Pancrea
33	chr12:123415800-123431600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:123417400-123427200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr12:123417400-123441800	Weak transcription	Ovary	ovary
36	chr12:123417600-123446200	Weak transcription	Fetal Lung	lung
37	chr12:123417800-123426600	Weak transcription	HepG2	liver
38	chr12:123417800-123427400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:123418000-123427400	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:123418400-123427200	Weak transcription	HUVEC	blood vessel
41	chr12:123419400-123425000	Strong transcription	Fetal Stomach	stomach
42	chr12:123419600-123425400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:123419600-123425800	Strong transcription	Brain Angular Gyrus	brain
44	chr12:123420000-123425200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr12:123420200-123424400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:123420200-123424600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:123420200-123427400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:123420400-123425600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:123420400-123425600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:123420400-123425600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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