Variant report

Variant	rs1392142
Chromosome Location	chr12:122887499-122887500
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr12:122886671-122887614	A549	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122887097..122891186-chr12:122896000..122898774,4	MCF-7	breast:
2	chr12:122884037..122886288-chr12:122886362..122887867,2	K562	blood:
3	chr12:122887135..122888989-chr12:122893412..122896084,2	MCF-7	breast:
4	chr12:122879571..122888507-chr12:122899670..122909196,27	K562	blood:
5	chr12:122884122..122887585-chr12:122984218..122986985,3	MCF-7	breast:
6	chr12:122884617..122887526-chr12:122893743..122896381,3	K562	blood:

No data

Variant related genes	Relation type
CLIP1	TF binding region
ENSG00000130779	Chromatin interaction
ENSG00000033030	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10161184	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs10161488	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10744218	0.90[EUR][1000 genomes]
rs10744242	0.81[CHB][hapmap]
rs10773090	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs10773108	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10773117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10773162	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10773230	0.81[CHB][hapmap];0.87[GIH][hapmap]
rs10846714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10846852	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10846871	0.93[ASN][1000 genomes]
rs10846899	0.82[ASN][1000 genomes]
rs10846912	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs10846968	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs11057514	0.83[EUR][1000 genomes]
rs11057522	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs11057686	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11057813	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11057819	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11058272	0.87[EUR][1000 genomes]
rs1129167	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs11503023	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11610303	0.81[CHB][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap]
rs11830957	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12314537	0.90[EUR][1000 genomes]
rs12812332	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs12817342	0.86[CHB][hapmap]
rs12818177	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12819355	0.80[ASN][1000 genomes]
rs12828876	0.84[EUR][1000 genomes]
rs12829449	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1532579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553178	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2341438	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3825096	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4356269	0.86[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs4758657	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4758658	0.86[CHB][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs4758660	0.81[CHB][hapmap];0.84[GIH][hapmap]
rs4758664	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4758665	0.83[EUR][1000 genomes]
rs4758692	0.86[CHB][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs4758693	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4758695	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs61021925	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6416295	0.81[CHB][hapmap];0.84[GIH][hapmap]
rs6488947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6489014	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs6489051	0.81[CHB][hapmap]
rs6489056	0.87[GIH][hapmap]
rs7134381	0.81[CHB][hapmap]
rs7296680	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7298839	0.81[CHB][hapmap]
rs7305360	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7311573	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs7313121	0.90[EUR][1000 genomes]
rs7313284	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs7953204	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7955241	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7955513	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs7959550	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7961258	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7964981	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7970007	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7972832	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973480	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974160	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs7975492	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs7978119	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7978636	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs868181	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs9788228	0.95[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1392142	CCDC62	cis	cerebellum	SCAN
rs1392142	DYNLL1	cis	parietal	SCAN
rs1392142	DIABLO	cis	parietal	SCAN
rs1392142	NME2P1	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122860600-122905000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:122862800-122895600	Weak transcription	Small Intestine	intestine
3	chr12:122863400-122897400	Weak transcription	Fetal Brain Female	brain
4	chr12:122863400-122897800	Weak transcription	Brain Substantia Nigra	brain
5	chr12:122863800-122905000	Weak transcription	Dnd41	blood
6	chr12:122866600-122888400	Weak transcription	Gastric	stomach
7	chr12:122878800-122888400	Weak transcription	Primary T cells from cord blood	blood
8	chr12:122884400-122889800	Weak transcription	Aorta	Aorta
9	chr12:122884600-122888400	Weak transcription	Psoas Muscle	Psoas
10	chr12:122884600-122897600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:122884600-122905200	Weak transcription	Colonic Mucosa	Colon
12	chr12:122884800-122888400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:122885200-122887600	Weak transcription	Primary B cells from cord blood	blood
14	chr12:122885200-122887600	Enhancers	HMEC	breast
15	chr12:122885200-122887600	Enhancers	NHEK	skin
16	chr12:122885200-122887800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:122885200-122887800	Enhancers	Rectal Smooth Muscle	rectum
18	chr12:122885200-122888000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:122885200-122888000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:122885200-122888400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:122885200-122888400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr12:122885200-122888400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:122885200-122888400	Weak transcription	Fetal Muscle Leg	muscle
24	chr12:122885200-122888400	Weak transcription	Fetal Stomach	stomach
25	chr12:122885200-122888400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr12:122885200-122888400	Weak transcription	Spleen	Spleen
27	chr12:122885200-122889000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr12:122885200-122890000	Weak transcription	Fetal Intestine Large	intestine
29	chr12:122885200-122890400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr12:122885200-122890800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:122885200-122891200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:122885200-122891200	Weak transcription	Adipose Nuclei	Adipose
33	chr12:122885200-122891200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:122885200-122891600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:122885200-122891600	Weak transcription	Brain Angular Gyrus	brain
36	chr12:122885200-122893800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr12:122885200-122897800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr12:122885200-122897800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr12:122885200-122902400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:122885200-122902600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr12:122885200-122904600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr12:122885200-122905200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr12:122885200-122905400	Weak transcription	Fetal Thymus	thymus
44	chr12:122885200-122905400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr12:122885200-122906000	Weak transcription	Ovary	ovary
46	chr12:122885400-122888400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:122885400-122888400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:122885400-122891400	Weak transcription	Fetal Kidney	kidney
49	chr12:122885400-122891800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:122885400-122895400	Weak transcription	Fetal Lung	lung

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