Variant report

Variant	rs13058500
Chromosome Location	chr22:33115879-33115880
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:33115192..33117854-chr22:33156131..33157646,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10854627	0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10854628	0.87[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs11089591	1.00[ASN][1000 genomes]
rs12484015	1.00[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12484429	0.81[CHD][hapmap];0.82[ASN][1000 genomes]
rs13054529	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.99[ASN][1000 genomes]
rs1475978	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs1475979	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16991028	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs16991084	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs2899193	0.82[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3827339	0.87[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4821089	1.00[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5754227	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs725337	0.91[CHB][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs725338	0.82[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs7286819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7289865	0.81[ASN][1000 genomes]
rs7291198	0.87[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs7291871	0.86[ASN][1000 genomes]
rs731933	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs743741	0.93[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743742	0.81[ASW][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs743744	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs743745	0.87[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8136470	0.83[CHB][hapmap]
rs9619301	0.87[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs997120	0.87[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.86[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	nsv1064719	chr22:33028891-33159636	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13058500	RFPL1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33104400-33117000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr22:33110400-33116800	Weak transcription	NHDF-Ad	bronchial
3	chr22:33111000-33118600	Weak transcription	HSMMtube	muscle
4	chr22:33111400-33116800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr22:33112200-33121400	Enhancers	Fetal Thymus	thymus
6	chr22:33113000-33121600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr22:33113400-33120400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr22:33113800-33116800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr22:33113800-33116800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr22:33114000-33116400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr22:33114000-33116800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr22:33114200-33116400	Weak transcription	Spleen	Spleen
13	chr22:33114200-33116600	Weak transcription	NH-A	brain
14	chr22:33114200-33116600	Weak transcription	Osteobl	bone
15	chr22:33114200-33119400	Weak transcription	Esophagus	oesophagus
16	chr22:33114400-33116000	Weak transcription	Fetal Intestine Small	intestine
17	chr22:33114400-33116400	Weak transcription	Lung	lung
18	chr22:33114400-33116400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr22:33114400-33116600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr22:33114400-33116800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr22:33114400-33116800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr22:33114400-33116800	Weak transcription	Adipose Nuclei	Adipose
23	chr22:33114400-33116800	Weak transcription	Fetal Lung	lung
24	chr22:33114400-33116800	Weak transcription	Right Atrium	heart
25	chr22:33114400-33116800	Weak transcription	NHLF	lung
26	chr22:33114400-33117000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr22:33114400-33119000	Weak transcription	Small Intestine	intestine
28	chr22:33114400-33119400	Weak transcription	Left Ventricle	heart
29	chr22:33114400-33121400	Weak transcription	Colon Smooth Muscle	Colon
30	chr22:33114600-33116600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr22:33114600-33116600	Weak transcription	Fetal Stomach	stomach
32	chr22:33114600-33116600	Weak transcription	NHEK	skin
33	chr22:33114600-33121800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr22:33115000-33116600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr22:33115000-33116800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr22:33115000-33116800	Weak transcription	Placenta	Placenta
37	chr22:33115200-33117400	Enhancers	Fetal Muscle Leg	muscle
38	chr22:33115600-33116800	Enhancers	HepG2	liver
39	chr22:33115600-33119600	Enhancers	Thymus	Thymus
40	chr22:33115800-33116200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr22:33115800-33117400	Enhancers	Fetal Intestine Large	intestine
42	chr22:33115800-33119400	Enhancers	Dnd41	blood
43	chr22:33115800-33122200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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