Variant report

Variant	rs1532579
Chromosome Location	chr12:122886219-122886220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:122886023-122886223	K562	blood:	n/a	n/a
2	RAD21	chr12:122886053-122886324	HepG2	liver:	n/a	n/a
3	CTCF	chr12:122886078-122886252	K562	blood:	n/a	n/a
4	CTCF	chr12:122886063-122886245	HepG2	liver:	n/a	n/a
5	CTCF	chr12:122886081-122886230	GM19239	blood:	n/a	n/a
6	CTCF	chr12:122886120-122886270	K562	blood:	n/a	n/a
7	CTCF	chr12:122886140-122886290	GM12873	blood:	n/a	n/a
8	CTCF	chr12:122886120-122886270	GM12875	blood:	n/a	n/a
9	CTCF	chr12:122886120-122886270	WERI-Rb-1	eye:	n/a	n/a
10	CTCF	chr12:122886120-122886270	GM12864	blood:	n/a	n/a
11	RAD21	chr12:122886033-122886344	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr12:122886120-122886270	A549	lung:	n/a	n/a
13	RAD21	chr12:122886043-122886221	K562	blood:	n/a	n/a
14	RAD21	chr12:122886053-122886274	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr12:122886120-122886270	HEK293	kidney:	n/a	n/a
16	CTCF	chr12:122886100-122886231	Medullo	brain:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122884287..122886511-chr12:122976767..122978774,2	K562	blood:
2	chr12:122502325..122504629-chr12:122884627..122886356,2	K562	blood:
3	chr12:122883132..122886264-chr12:123235650..123239708,3	MCF-7	breast:
4	chr12:122878851..122886809-chr12:122904517..122908613,16	MCF-7	breast:
5	chr12:122879571..122888507-chr12:122899670..122909196,27	K562	blood:
6	chr12:122885715..122886229-chr12:122955925..122956837,2	K562	blood:
7	chr12:122877588..122886723-chr12:122904086..122910536,22	K562	blood:
8	chr12:122884122..122887585-chr12:122984218..122986985,3	MCF-7	breast:
9	chr12:122884270..122886424-chr12:123011596..123013122,2	MCF-7	breast:
10	chr12:122882564..122887396-chr12:122904302..122908331,13	MCF-7	breast:
11	chr12:122884617..122887526-chr12:122893743..122896381,3	K562	blood:
12	chr12:122883747..122886226-chr12:122990719..122993167,2	K562	blood:

No data

Variant related genes	Relation type
CLIP1	TF binding region
ENSG00000184445	Chromatin interaction
ENSG00000111011	Chromatin interaction
ENSG00000130779	Chromatin interaction
ENSG00000252192	Chromatin interaction
ENSG00000139726	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]
rs1392142	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	0.97[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];0.85[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];0.98[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	0.96[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
rs1532579	CCDC62	cis	cerebellum	SCAN
rs1532579	DYNLL1	cis	parietal	SCAN
rs1532579	NME2P1	cis	cerebellum	SCAN
rs1532579	DIABLO	cis	parietal	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	chr12:122884000-122886600	Enhancers	Pancreas	Pancrea
9	chr12:122884400-122889800	Weak transcription	Aorta	Aorta
10	chr12:122884600-122888400	Weak transcription	Psoas Muscle	Psoas
11	chr12:122884600-122897600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:122884600-122905200	Weak transcription	Colonic Mucosa	Colon
13	chr12:122884800-122888400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:122885200-122886800	Weak transcription	Brain Anterior Caudate	brain
15	chr12:122885200-122886800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr12:122885200-122887400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr12:122885200-122887400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:122885200-122887400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:122885200-122887600	Weak transcription	Primary B cells from cord blood	blood
20	chr12:122885200-122887600	Enhancers	HMEC	breast
21	chr12:122885200-122887600	Enhancers	NHEK	skin
22	chr12:122885200-122887800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:122885200-122887800	Enhancers	Rectal Smooth Muscle	rectum
24	chr12:122885200-122888000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:122885200-122888000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:122885200-122888400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:122885200-122888400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr12:122885200-122888400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:122885200-122888400	Weak transcription	Fetal Muscle Leg	muscle
30	chr12:122885200-122888400	Weak transcription	Fetal Stomach	stomach
31	chr12:122885200-122888400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:122885200-122888400	Weak transcription	Spleen	Spleen
33	chr12:122885200-122889000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr12:122885200-122890000	Weak transcription	Fetal Intestine Large	intestine
35	chr12:122885200-122890400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr12:122885200-122890800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:122885200-122891200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:122885200-122891200	Weak transcription	Adipose Nuclei	Adipose
39	chr12:122885200-122891200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:122885200-122891600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:122885200-122891600	Weak transcription	Brain Angular Gyrus	brain
42	chr12:122885200-122893800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr12:122885200-122897800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr12:122885200-122897800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr12:122885200-122902400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:122885200-122902600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr12:122885200-122904600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr12:122885200-122905200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr12:122885200-122905400	Weak transcription	Fetal Thymus	thymus
50	chr12:122885200-122905400	Weak transcription	Rectal Mucosa Donor 29	rectum

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