Variant report

Variant	rs2283852
Chromosome Location	chr22:29781445-29781446
allele	G/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:29780907..29784157-chr22:29912302..29916422,4	MCF-7	breast:
2	chr22:29704896..29707829-chr22:29780262..29782390,2	MCF-7	breast:
3	chr22:29781310..29782787-chr22:29913055..29914130,15	MCF-7	breast:
4	chr22:29780492..29782846-chr22:29865528..29867159,2	MCF-7	breast:
5	chr22:29739232..29740930-chr22:29780922..29783404,2	MCF-7	breast:
6	chr22:29774954..29777707-chr22:29779123..29781815,2	K562	blood:
7	chr22:29770782..29772689-chr22:29780811..29782872,2	K562	blood:
8	chr22:29781329..29782720-chr22:29913118..29914020,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185340	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1807503	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2002566	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267135	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2267136	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283853	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2283854	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301291	0.80[CHD][hapmap]
rs2348468	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857466	0.83[JPT][hapmap]
rs2881921	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34234634	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs378720	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3788412	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3963293	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4034938	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap]
rs4820809	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4823032	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5752905	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5752906	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5752907	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763138	0.81[CHD][hapmap]
rs5763144	0.88[ASN][1000 genomes]
rs5763171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763172	0.85[CEU][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5763173	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763179	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763182	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5763189	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5763190	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5997467	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6006103	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6006104	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6006108	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6006109	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6006112	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6006113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6006115	1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs714962	0.81[EUR][1000 genomes]
rs737883	0.89[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs909798	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs9613878	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
4	nsv914961	chr22:29755888-29817506	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv914962	chr22:29755888-29823768	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	esv2580719	chr22:29759273-29816494	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	esv3498689	chr22:29763576-29812598	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	esv3498690	chr22:29763576-29812598	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	esv3382633	chr22:29764347-29814462	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv459868	chr22:29767925-29807855	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	nsv459869	chr22:29767925-29807855	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv588882	chr22:29767925-29807855	Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
14	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2283852	NEFH	cis	parietal	SCAN
rs2283852	NF2	cis	parietal	SCAN
rs2283852	TPST2	cis	cerebellum	SCAN
rs2283852	DUSP18	cis	parietal	SCAN
rs2283852	PIWIL3	cis	cerebellum	SCAN
rs2283852	SRRD	cis	parietal	SCAN
rs2283852	NIPSNAP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29741000-29782800	Weak transcription	Hela-S3	cervix
2	chr22:29755000-29783800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:29755200-29782800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr22:29755400-29783600	Weak transcription	Fetal Kidney	kidney
5	chr22:29756000-29783600	Weak transcription	Right Ventricle	heart
6	chr22:29756000-29783800	Weak transcription	Ovary	ovary
7	chr22:29756400-29782600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr22:29765400-29782600	Weak transcription	Colon Smooth Muscle	Colon
9	chr22:29765400-29783600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr22:29765600-29783600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr22:29765600-29783600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:29765800-29782800	Weak transcription	NHDF-Ad	bronchial
13	chr22:29766200-29783600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr22:29767200-29783600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr22:29767400-29783400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr22:29767400-29783600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr22:29768000-29783600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr22:29768000-29783800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr22:29769200-29783600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr22:29770400-29782600	Strong transcription	Primary T cells from cord blood	blood
21	chr22:29772400-29783000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr22:29772600-29782400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr22:29772600-29783400	Weak transcription	HSMMtube	muscle
24	chr22:29772800-29782800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr22:29773600-29783600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr22:29773600-29783600	Weak transcription	HSMM	muscle
27	chr22:29774000-29783600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr22:29774200-29782000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr22:29774200-29783000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr22:29774200-29783600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr22:29774200-29784000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr22:29774600-29782200	Weak transcription	Psoas Muscle	Psoas
33	chr22:29775400-29781600	Strong transcription	Stomach Smooth Muscle	stomach
34	chr22:29776200-29782000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr22:29776400-29783600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr22:29776800-29782800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr22:29777000-29781600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr22:29777000-29782200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr22:29777000-29782800	Weak transcription	Esophagus	oesophagus
40	chr22:29777000-29783400	Weak transcription	Right Atrium	heart
41	chr22:29777000-29783600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr22:29777200-29782200	Weak transcription	HMEC	breast
43	chr22:29777600-29781600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr22:29777600-29782000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr22:29777800-29781600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr22:29778000-29781800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr22:29778000-29782600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr22:29778000-29783000	Enhancers	Liver	Liver
49	chr22:29778400-29783600	Enhancers	HepG2	liver
50	chr22:29778600-29781600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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