Variant report

Variant	rs4820983
Chromosome Location	chr22:31929654-31929655
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	chr22:31890839..31893648-chr22:31927423..31929799,2	MCF-7	breast:
2	chr22:31928865..31930656-chr22:31938813..31940821,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198089	Chromatin interaction
ENSG00000184708	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11704494	0.82[AFR][1000 genomes]
rs12170867	0.81[JPT][hapmap]
rs12171042	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs12484606	0.89[EUR][1000 genomes]
rs12485048	0.87[CHB][hapmap]
rs13056823	0.90[EUR][1000 genomes]
rs1543416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1916	0.88[LWK][hapmap];0.92[MKK][hapmap];0.89[YRI][hapmap]
rs2006771	0.86[YRI][hapmap]
rs2012451	0.80[LWK][hapmap]
rs2024747	0.86[JPT][hapmap]
rs2092905	0.81[JPT][hapmap]
rs2295242	0.81[JPT][hapmap]
rs2295251	0.95[CEU][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap]
rs2387	0.81[JPT][hapmap]
rs3818134	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4535154	0.88[EUR][1000 genomes]
rs4820048	0.83[LWK][hapmap];0.86[YRI][hapmap]
rs4820974	0.80[LWK][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap]
rs4820976	0.88[EUR][1000 genomes]
rs4820978	0.92[EUR][1000 genomes]
rs4820979	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs4820980	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4820981	0.88[EUR][1000 genomes]
rs4820982	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749286	0.82[JPT][hapmap]
rs5749287	0.87[EUR][1000 genomes]
rs5749293	0.86[JPT][hapmap]
rs5749298	0.82[JPT][hapmap]
rs5749303	0.81[JPT][hapmap]
rs5749304	0.84[ASW][hapmap];0.82[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs5749306	0.81[JPT][hapmap]
rs5753659	0.82[JPT][hapmap]
rs5753667	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs5753669	0.82[JPT][hapmap]
rs5753671	0.82[JPT][hapmap]
rs5753680	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5753681	0.86[JPT][hapmap]
rs5753686	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5753734	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap]
rs5997971	0.82[YRI][hapmap]
rs5997988	0.81[LWK][hapmap]
rs5998002	0.83[LWK][hapmap];0.90[MKK][hapmap];0.82[YRI][hapmap]
rs5998011	0.89[EUR][1000 genomes]
rs5998032	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5998035	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5998042	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5998054	0.82[TSI][hapmap]
rs7284622	0.82[JPT][hapmap]
rs7287937	0.83[YRI][hapmap]
rs7289075	1.00[CEU][hapmap]
rs7289941	0.83[YRI][hapmap]
rs7291918	0.89[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap]
rs738656	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs738702	0.81[JPT][hapmap]
rs761746	0.84[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap]
rs8461	0.85[GIH][hapmap]
rs9606848	0.82[JPT][hapmap]
rs9609296	0.82[JPT][hapmap]
rs9609297	0.82[JPT][hapmap]
rs9609304	0.82[JPT][hapmap]
rs9621279	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9956	0.94[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap]

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	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv1059314	chr22:31893613-31936088	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv914978	chr22:31897795-31942770	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4820983	SFI1	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31893200-31934800	Weak transcription	Ovary	ovary
2	chr22:31893400-31971200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr22:31893600-31934800	Weak transcription	Pancreas	Pancrea
4	chr22:31893600-31946600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr22:31893600-31970000	Weak transcription	Colonic Mucosa	Colon
6	chr22:31893800-31934800	Weak transcription	HMEC	breast
7	chr22:31893800-31945600	Weak transcription	Brain Anterior Caudate	brain
8	chr22:31894000-31946600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr22:31894000-31946600	Weak transcription	Fetal Brain Female	brain
10	chr22:31895400-31931200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr22:31898000-31934800	Weak transcription	Spleen	Spleen
12	chr22:31900800-31940800	Weak transcription	NHEK	skin
13	chr22:31903400-31934400	Weak transcription	Hela-S3	cervix
14	chr22:31904400-31944200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr22:31905200-31957200	Weak transcription	A549	lung
16	chr22:31905600-31946200	Weak transcription	Esophagus	oesophagus
17	chr22:31907400-31946400	Weak transcription	Brain Germinal Matrix	brain
18	chr22:31907400-31946600	Weak transcription	Left Ventricle	heart
19	chr22:31907600-31946200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr22:31907800-31934400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr22:31907800-31942800	Weak transcription	Fetal Intestine Large	intestine
22	chr22:31908200-31935200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr22:31910200-31934800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr22:31911600-31934600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr22:31911800-31934800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr22:31911800-31946000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr22:31917800-31933000	Weak transcription	K562	blood
28	chr22:31918000-31940600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr22:31920400-31930000	Strong transcription	Primary T cells from cord blood	blood
30	chr22:31920800-31933000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr22:31921800-31942800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr22:31922200-31929800	Strong transcription	Dnd41	blood
33	chr22:31923000-31945800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr22:31923400-31930000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr22:31924000-31943600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr22:31924200-31929800	Strong transcription	Thymus	Thymus
37	chr22:31924600-31930800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr22:31925000-31934600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr22:31925000-31946200	Weak transcription	Adipose Nuclei	Adipose
40	chr22:31925200-31942000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr22:31925600-31933200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr22:31925600-31942800	Weak transcription	Lung	lung
43	chr22:31925800-31933000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr22:31925800-31934800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr22:31925800-31934800	Weak transcription	Gastric	stomach
46	chr22:31925800-31936800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr22:31925800-31936800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr22:31925800-31957200	Weak transcription	Brain Angular Gyrus	brain
49	chr22:31926000-31940800	Weak transcription	Fetal Intestine Small	intestine
50	chr22:31926400-31930000	Enhancers	HepG2	liver

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