Variant report

Variant	rs715589
Chromosome Location	chr22:29743779-29743780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29742016..29743805-chr22:29745307..29748693,3	MCF-7	breast:
2	chr22:29663374..29666132-chr22:29741541..29744450,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182944	Chromatin interaction
ENSG00000100263	Chromatin interaction
ENSG00000100280	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2267134	0.91[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.86[ASN][1000 genomes]
rs2283851	0.82[ASN][1000 genomes]
rs3747142	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3747146	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3761426	0.88[CEU][hapmap];0.81[GIH][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs418267	0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6006093	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9613857	0.83[EUR][1000 genomes]
rs9613860	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9613863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9613864	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9613877	0.91[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs715589	RFPL1	cis	Liver	GTEx
rs715589	RFPL1	cis	multi-tissue	Pritchard
rs715589	OSBP2	cis	cerebellum	SCAN
rs715589	RFPL1	cis	parietal	SCAN
rs715589	PISD	cis	parietal	SCAN
rs715589	RFPL3	cis	Liver	GTEx
rs715589	NEFH	cis	cerebellum	SCAN
rs715589	RASL10A	cis	cerebellum	SCAN
rs715589	PITPNB	cis	cerebellum	SCAN
rs715589	SMARCB1	cis	cerebellum	SCAN
rs715589	SEC14L4	cis	parietal	SCAN
rs715589	NEFH	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29721400-29746800	Strong transcription	Fetal Intestine Small	intestine
2	chr22:29721800-29756800	Strong transcription	Primary T cells from cord blood	blood
3	chr22:29722000-29747000	Strong transcription	Duodenum Mucosa	Duodenum
4	chr22:29722000-29759200	Strong transcription	Dnd41	blood
5	chr22:29722000-29759800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr22:29722200-29755800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr22:29722200-29756400	Strong transcription	Thymus	Thymus
8	chr22:29722200-29756600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr22:29722200-29759800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr22:29722400-29756800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr22:29722400-29758400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr22:29722600-29751200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr22:29722600-29753200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr22:29722600-29755400	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr22:29722600-29756000	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr22:29722600-29757200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr22:29722600-29758000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr22:29722600-29758800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr22:29723000-29758800	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr22:29723000-29765000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr22:29725400-29756200	Strong transcription	Primary B cells from cord blood	blood
22	chr22:29727400-29756200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr22:29727600-29746600	Strong transcription	Fetal Intestine Large	intestine
24	chr22:29728000-29756200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr22:29728400-29755400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr22:29731600-29753200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr22:29731800-29755400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr22:29734000-29744600	Weak transcription	Stomach Mucosa	stomach
29	chr22:29737800-29747000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr22:29738200-29747600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr22:29738200-29755800	Strong transcription	Spleen	Spleen
32	chr22:29738600-29743800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr22:29739000-29743800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr22:29739000-29762800	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr22:29739200-29755400	Weak transcription	Right Atrium	heart
36	chr22:29739400-29755600	Strong transcription	Gastric	stomach
37	chr22:29739600-29744200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr22:29739800-29757200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr22:29740200-29755600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr22:29740200-29756400	Strong transcription	Fetal Thymus	thymus
41	chr22:29740400-29744200	Weak transcription	Fetal Lung	lung
42	chr22:29740400-29745800	Weak transcription	A549	lung
43	chr22:29740600-29759000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr22:29740800-29748400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr22:29740800-29756000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr22:29740800-29759000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr22:29741000-29743800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr22:29741000-29745200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr22:29741000-29752400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr22:29741000-29755200	Strong transcription	Fetal Stomach	stomach

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