Variant report

Variant	rs5753734
Chromosome Location	chr22:32028721-32028722
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	22:32012966-32043914..22:32347255-32351014	K562	blood:
2	22:31936958-31958600..22:32012966-32043914	GM12878	blood:
3	chr22:31884997..31887735-chr22:32023066..32028730,7	MCF-7	breast:
4	chr22:32027036..32029342-chr22:32032143..32033844,2	MCF-7	breast:
5	22:32012966-32043914..22:32513817-32522138	K562	blood:
6	22:31829733-31836635..22:32012966-32043914	GM12878	blood:
7	22:32012966-32043914..22:32665993-32670527	K562	blood:
8	chr22:31796576..31798824-chr22:32026967..32029510,2	K562	blood:
9	chr22:31971863..31974758-chr22:32025154..32029039,5	MCF-7	breast:
10	22:31930706-31935473..22:32012966-32043914	GM12878	blood:
11	22:32012966-32043914..22:32529813-32538538	K562	blood:
12	chr22:32025758..32028730-chr22:32031717..32035857,4	K562	blood:
13	chr22:31795193..31796801-chr22:32026385..32029380,2	MCF-7	breast:
14	22:32012966-32043914..22:32846948-32860159	K562	blood:
15	chr22:31889712..31892682-chr22:32027808..32029644,2	MCF-7	breast:
16	chr22:31884998..31887254-chr22:32026687..32028800,2	K562	blood:
17	chr22:32026689..32028779-chr22:32033425..32035914,3	K562	blood:
18	chr22:32027217..32028828-chr22:32033884..32035485,2	MCF-7	breast:
19	chr22:31883675..31887496-chr22:32025240..32029301,5	K562	blood:
20	chr22:31982333..31984122-chr22:32028532..32031400,2	MCF-7	breast:
21	chr22:31958875..31961811-chr22:32027409..32029066,2	MCF-7	breast:
22	22:32012966-32043914..22:32360288-32405313	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238910	Chromatin interaction
ENSG00000232707	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000185721	Chromatin interaction
ENSG00000184459	Chromatin interaction
ENSG00000198089	Chromatin interaction
ENSG00000239674	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000230866	Chromatin interaction
ENSG00000224050	Chromatin interaction
ENSG00000240647	Chromatin interaction
ENSG00000214093	Chromatin interaction
ENSG00000229169	Chromatin interaction
ENSG00000234479	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1044085	0.85[JPT][hapmap]
rs12170867	0.86[JPT][hapmap]
rs12171042	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12627933	0.87[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs140078	0.83[ASW][hapmap];0.89[MEX][hapmap]
rs140081	0.83[ASW][hapmap];0.88[MEX][hapmap]
rs14034	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1543416	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap]
rs2092905	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap]
rs2236033	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2295242	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2295251	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2387	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3804087	0.83[ASW][hapmap];0.89[MEX][hapmap]
rs3818134	1.00[CEU][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs4820051	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs4820979	1.00[CEU][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs4820980	1.00[CEU][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs4820982	1.00[CEU][hapmap]
rs4820983	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap]
rs5749293	0.80[JPT][hapmap]
rs5749303	0.86[JPT][hapmap]
rs5749304	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs5749306	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap]
rs5753667	1.00[CEU][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs5753681	0.80[JPT][hapmap]
rs5753686	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs5753691	0.84[JPT][hapmap];0.83[MEX][hapmap]
rs5753714	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs5753732	0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs5753733	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5994415	0.84[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs5998042	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs5998054	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs5998086	0.83[ASW][hapmap];0.89[MEX][hapmap]
rs7289075	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7291918	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs738656	1.00[CEU][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs738684	0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.87[ASN][1000 genomes]
rs738702	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs760908	0.83[ASW][hapmap]
rs761746	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs761747	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8461	0.88[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes]
rs9621279	0.83[EUR][1000 genomes]
rs9956	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][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	nsv829176	chr22:31998223-32029556	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2830290	chr22:32011225-32057964	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5753734	SFI1	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32027200-32042400	Weak transcription	A549	lung
2	chr22:32027200-32042600	Weak transcription	Thymus	Thymus
3	chr22:32027200-32043400	Weak transcription	Aorta	Aorta
4	chr22:32027400-32028800	Weak transcription	NHEK	skin
5	chr22:32027400-32029400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr22:32027400-32029400	Genic enhancers	Placenta	Placenta
7	chr22:32027400-32029800	Weak transcription	Liver	Liver
8	chr22:32027400-32029800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr22:32027400-32030000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr22:32027400-32033600	Weak transcription	Fetal Kidney	kidney
11	chr22:32027400-32034000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr22:32027400-32034000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr22:32027400-32042200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr22:32027400-32042800	Weak transcription	Fetal Lung	lung
15	chr22:32027600-32029400	Genic enhancers	Primary monocytes fromperipheralblood	blood
16	chr22:32027600-32029800	Weak transcription	Hela-S3	cervix
17	chr22:32027600-32030000	Genic enhancers	Fetal Intestine Small	intestine
18	chr22:32027600-32030000	Weak transcription	Stomach Mucosa	stomach
19	chr22:32027600-32030200	Weak transcription	HMEC	breast
20	chr22:32027600-32031600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr22:32027600-32031800	Weak transcription	Psoas Muscle	Psoas
22	chr22:32027600-32033400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr22:32027600-32033400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr22:32027600-32033400	Weak transcription	Gastric	stomach
25	chr22:32027600-32033400	Weak transcription	Right Atrium	heart
26	chr22:32027600-32033600	Weak transcription	Brain Anterior Caudate	brain
27	chr22:32027600-32033600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr22:32027600-32035600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr22:32027600-32035800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr22:32027600-32037000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr22:32027600-32040600	Weak transcription	Ovary	ovary
32	chr22:32027600-32042000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr22:32027600-32042000	Weak transcription	NH-A	brain
34	chr22:32027600-32042200	Weak transcription	Brain Germinal Matrix	brain
35	chr22:32027600-32043200	Weak transcription	HSMMtube	muscle
36	chr22:32027600-32044800	Weak transcription	Small Intestine	intestine
37	chr22:32027800-32029200	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr22:32027800-32029400	Genic enhancers	Monocytes-CD14+_RO01746	blood
39	chr22:32027800-32029600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr22:32027800-32029600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr22:32027800-32029600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr22:32027800-32029600	Weak transcription	Dnd41	blood
43	chr22:32027800-32029600	Weak transcription	K562	blood
44	chr22:32027800-32029800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr22:32027800-32029800	Enhancers	GM12878-XiMat	blood
46	chr22:32027800-32029800	Weak transcription	HepG2	liver
47	chr22:32027800-32030000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
48	chr22:32027800-32030000	Weak transcription	Fetal Thymus	thymus
49	chr22:32027800-32030200	Weak transcription	Esophagus	oesophagus
50	chr22:32027800-32031600	Weak transcription	Pancreas	Pancrea

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