Variant report

Variant	rs7553602
Chromosome Location	chr1:154529421-154529422
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154529298-154529473	HUVEC	blood vessel:	n/a	n/a
2	MXI1	chr1:154528662-154532574	SK-N-SH	brain:	n/a	chr1:154531305-154531314
3	MXI1	chr1:154528613-154530379	IMR90	lung:	n/a	n/a
4	POLR2A	chr1:154529373-154529463	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154528419..154530769-chr1:154535384..154537634,2	MCF-7	breast:
2	chr1:154460459..154462764-chr1:154527677..154529936,2	K562	blood:
3	chr1:154458190..154460389-chr1:154527899..154530840,2	K562	blood:
4	chr1:154191162..154194521-chr1:154529038..154532016,3	MCF-7	breast:
5	chr1:154528898..154533098-chr1:154907799..154911445,7	MCF-7	breast:
6	chr1:154529028..154532359-chr1:155034427..155037689,4	MCF-7	breast:
7	chr1:154529257..154532572-chr1:154598516..154601356,4	MCF-7	breast:
8	chr1:154529336..154531391-chr1:154925736..154927605,2	MCF-7	breast:
9	chr1:154529223..154531101-chr1:154799055..154800739,2	K562	blood:
10	chr1:154528881..154534687-chr1:154578685..154583746,8	MCF-7	breast:
11	chr1:154528624..154530149-chr1:155054658..155056691,2	MCF-7	breast:

No data

Variant related genes	Relation type
UBE2Q1	TF binding region
ENSG00000243364	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000160710	Chromatin interaction
ENSG00000270361	Chromatin interaction
ENSG00000163344	Chromatin interaction
ENSG00000251246	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000163346	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000169291	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10159236	1.00[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs10752642	1.00[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs10752643	0.94[EUR][1000 genomes]
rs10908844	0.94[EUR][1000 genomes]
rs10908846	0.94[EUR][1000 genomes]
rs11265618	1.00[CEU][hapmap]
rs11265627	1.00[CEU][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs11265629	0.88[EUR][1000 genomes]
rs11265634	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12118074	0.93[EUR][1000 genomes]
rs12124333	0.93[EUR][1000 genomes]
rs14021	1.00[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs16836054	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4074436	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs41302545	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4131514	0.94[EUR][1000 genomes]
rs4269769	0.94[EUR][1000 genomes]
rs4288587	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4307559	0.89[EUR][1000 genomes]
rs4308966	0.82[EUR][1000 genomes]
rs4329505	1.00[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs4345796	0.80[EUR][1000 genomes]
rs4474240	1.00[CEU][hapmap];0.81[GIH][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs4518898	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4575077	0.94[EUR][1000 genomes]
rs4585969	0.94[EUR][1000 genomes]
rs4845374	1.00[CEU][hapmap]
rs4845626	1.00[CEU][hapmap]
rs4845634	0.94[EUR][1000 genomes]
rs4845635	0.93[EUR][1000 genomes]
rs4845636	0.93[EUR][1000 genomes]
rs4845640	0.94[EUR][1000 genomes]
rs4845641	0.94[EUR][1000 genomes]
rs4845643	0.89[EUR][1000 genomes]
rs4845644	0.95[EUR][1000 genomes]
rs4845648	0.95[EUR][1000 genomes]
rs4845652	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs56047170	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56233546	0.94[EUR][1000 genomes]
rs61811362	0.95[EUR][1000 genomes]
rs61811370	0.81[ASN][1000 genomes]
rs61811371	0.81[ASN][1000 genomes]
rs61812626	0.80[EUR][1000 genomes]
rs61812631	0.94[EUR][1000 genomes]
rs61812654	0.95[EUR][1000 genomes]
rs6427716	1.00[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs6427720	0.89[EUR][1000 genomes]
rs6427722	0.94[EUR][1000 genomes]
rs6427724	0.89[EUR][1000 genomes]
rs6656395	0.94[EUR][1000 genomes]
rs6660775	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6662503	0.92[EUR][1000 genomes]
rs6670375	1.00[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs6687112	1.00[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs6689710	0.85[EUR][1000 genomes]
rs6691727	1.00[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs6696177	0.88[EUR][1000 genomes]
rs6697103	0.94[EUR][1000 genomes]
rs6697115	0.94[EUR][1000 genomes]
rs6701586	0.94[EUR][1000 genomes]
rs6703672	0.85[EUR][1000 genomes]
rs72698167	0.94[EUR][1000 genomes]
rs7513603	1.00[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs7526247	0.88[EUR][1000 genomes]
rs7539745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7543174	0.94[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7550664	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427076	0.95[EUR][1000 genomes]
rs9427082	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9427415	1.00[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7553602	CDC42SE1	cis	cerebellum	SCAN
rs7553602	SNX27	cis	parietal	SCAN
rs7553602	RPTN	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154528200-154529600	Genic enhancers	Lung	lung
2	chr1:154528400-154529600	Weak transcription	Esophagus	oesophagus
3	chr1:154528400-154530600	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr1:154528600-154529600	Genic enhancers	Primary B cells from peripheral blood	blood
5	chr1:154528600-154529600	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr1:154528600-154529600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:154528600-154529600	Enhancers	Stomach Mucosa	stomach
8	chr1:154528600-154529800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:154528600-154529800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:154528600-154529800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:154528600-154529800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:154528600-154529800	Enhancers	Gastric	stomach
13	chr1:154528600-154530000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr1:154528600-154530000	Flanking Active TSS	HSMMtube	muscle
15	chr1:154528600-154530200	Flanking Active TSS	HMEC	breast
16	chr1:154528600-154530400	Flanking Active TSS	Hela-S3	cervix
17	chr1:154528600-154530600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:154528600-154530600	Flanking Active TSS	HUVEC	blood vessel
19	chr1:154528800-154529600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:154528800-154529600	Enhancers	Primary B cells from cord blood	blood
21	chr1:154528800-154529600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:154528800-154529600	Enhancers	Aorta	Aorta
23	chr1:154528800-154529600	Enhancers	Fetal Thymus	thymus
24	chr1:154528800-154529600	Flanking Active TSS	HSMM	muscle
25	chr1:154528800-154529600	Flanking Active TSS	NHDF-Ad	bronchial
26	chr1:154528800-154529600	Active TSS	NHLF	lung
27	chr1:154528800-154529800	Flanking Active TSS	HepG2	liver
28	chr1:154528800-154530000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:154528800-154530000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr1:154528800-154530000	Flanking Active TSS	NH-A	brain
31	chr1:154528800-154530200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr1:154528800-154530200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr1:154528800-154530200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:154528800-154530200	Flanking Active TSS	Colon Smooth Muscle	Colon
35	chr1:154528800-154530200	Flanking Active TSS	Fetal Heart	heart
36	chr1:154528800-154530400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr1:154528800-154530400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:154528800-154530400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:154528800-154530600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:154528800-154530600	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr1:154528800-154530600	Transcr. at gene 5' and 3'	Dnd41	blood
42	chr1:154528800-154530600	Flanking Active TSS	NHEK	skin
43	chr1:154528800-154530800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:154528800-154531600	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr1:154528800-154532000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:154529000-154529600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:154529000-154529600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:154529000-154529600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:154529000-154529600	Active TSS	Fetal Kidney	kidney
50	chr1:154529000-154529800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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