Variant report

Variant	rs1154514
Chromosome Location	chr12:122374888-122374889
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	chr12:122325828..122328717-chr12:122372797..122374931,2	K562	blood:

Variant related genes	Relation type
ENSG00000110801	Chromatin interaction
ENSG00000256950	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10840630	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840631	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840632	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840633	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840637	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs11043223	1.00[CHD][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap]
rs11043225	1.00[ASN][1000 genomes]
rs11043233	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043242	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs11043243	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11043244	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043246	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043251	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043271	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043275	0.80[EUR][1000 genomes]
rs11043278	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043280	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043288	1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs1154517	0.82[YRI][hapmap]
rs11612028	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615980	0.81[EUR][1000 genomes]
rs1169070	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1169071	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1177588	0.85[YRI][hapmap]
rs11833399	1.00[CHD][hapmap]
rs12369331	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809676	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817066	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12822775	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12823194	1.00[ASN][1000 genomes]
rs12824593	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12825161	1.00[ASN][1000 genomes]
rs12827036	1.00[CHD][hapmap]
rs12827452	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1375653	0.86[YRI][hapmap]
rs1375654	0.82[YRI][hapmap]
rs1375655	0.86[YRI][hapmap]
rs1630699	0.86[YRI][hapmap]
rs1678952	0.90[YRI][hapmap]
rs1678953	0.86[YRI][hapmap]
rs1720030	0.86[YRI][hapmap]
rs1720033	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1720037	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167067	1.00[ASN][1000 genomes]
rs34159444	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34906460	1.00[ASN][1000 genomes]
rs3847694	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs3887885	0.81[EUR][1000 genomes]
rs4069666	0.82[YRI][hapmap]
rs529736	0.86[YRI][hapmap]
rs66751701	1.00[ASN][1000 genomes]
rs7132055	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137218	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs7309024	0.81[EUR][1000 genomes]
rs7313252	0.96[CEU][hapmap]
rs73217776	1.00[ASN][1000 genomes]
rs9739381	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1154514	C19orf44	trans	parietal	SCAN
rs1154514	WDR66	cis	cerebellum	SCAN
rs1154514	CCDC60	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122357000-122380400	Weak transcription	Gastric	stomach
2	chr12:122357000-122383600	Weak transcription	Primary T cells from cord blood	blood
3	chr12:122363000-122384800	Weak transcription	Psoas Muscle	Psoas
4	chr12:122363000-122393400	Weak transcription	Brain Angular Gyrus	brain
5	chr12:122363200-122384600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:122363400-122375000	Weak transcription	Spleen	Spleen
7	chr12:122363400-122377000	Weak transcription	Fetal Intestine Small	intestine
8	chr12:122363600-122375000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:122363600-122375000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:122363600-122375400	Weak transcription	Right Atrium	heart
11	chr12:122363600-122377400	Weak transcription	Fetal Brain Female	brain
12	chr12:122363600-122383600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:122363600-122383800	Weak transcription	Fetal Brain Male	brain
14	chr12:122363600-122385600	Weak transcription	Fetal Lung	lung
15	chr12:122363600-122392200	Weak transcription	Left Ventricle	heart
16	chr12:122363600-122398600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:122363600-122408000	Weak transcription	Right Ventricle	heart
18	chr12:122365400-122375000	Weak transcription	Lung	lung
19	chr12:122365600-122385800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr12:122365600-122393400	Weak transcription	Brain Substantia Nigra	brain
21	chr12:122365800-122375000	Weak transcription	Liver	Liver
22	chr12:122365800-122390200	Weak transcription	HUVEC	blood vessel
23	chr12:122365800-122405000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:122366000-122376800	Weak transcription	HMEC	breast
25	chr12:122369600-122375800	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:122369600-122376000	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr12:122369600-122376000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:122369800-122376800	Weak transcription	Placenta	Placenta
29	chr12:122370000-122375000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:122370600-122387800	Weak transcription	NHDF-Ad	bronchial
31	chr12:122370600-122403200	Weak transcription	Fetal Kidney	kidney
32	chr12:122370800-122375000	Weak transcription	Osteobl	bone
33	chr12:122371200-122375200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:122371400-122375000	Weak transcription	Aorta	Aorta
35	chr12:122371800-122375200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:122372000-122375800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:122372000-122376000	Strong transcription	NHLF	lung
38	chr12:122372200-122375200	Weak transcription	NHEK	skin
39	chr12:122372200-122379600	Weak transcription	NH-A	brain
40	chr12:122372200-122396400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr12:122372400-122375000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:122372400-122375000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:122372400-122375000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:122372400-122376200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:122372400-122377400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr12:122372400-122378600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr12:122372600-122375000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr12:122372800-122375000	Weak transcription	Fetal Muscle Leg	muscle
49	chr12:122372800-122393600	Weak transcription	Brain Hippocampus Middle	brain
50	chr12:122373600-122375200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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