Variant report

Variant	rs2267156
Chromosome Location	chr22:30811112-30811113
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30803407..30806947-chr22:30810704..30813525,4	K562	blood:
2	chr22:30809702..30812364-chr22:30817775..30822138,4	MCF-7	breast:
3	chr22:30802321..30807877-chr22:30810760..30815440,6	MCF-7	breast:
4	chr22:30791955..30794186-chr22:30808827..30811485,2	MCF-7	breast:
5	chr22:30808620..30811901-chr22:30819601..30823234,3	K562	blood:

Variant related genes	Relation type
ENSG00000242114	Chromatin interaction
ENSG00000249590	Chromatin interaction
ENSG00000100003	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1005835	0.84[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1010324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11089442	0.82[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs11089447	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11089448	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11089449	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11703867	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11705639	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12171261	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2072160	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2074731	0.91[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2267154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283866	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2283870	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2283871	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2299827	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2839998	0.91[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57940170	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5994294	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5994305	0.92[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5994306	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5997637	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997646	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61583714	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71331235	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7288366	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7289360	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7290317	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8141656	0.91[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9619096	0.91[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs9619098	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9619105	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9620984	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2267156	SYN3	cis	parietal	SCAN
rs2267156	NIPSNAP1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30794000-30816600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:30794000-30818000	Weak transcription	Right Atrium	heart
3	chr22:30794400-30811800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr22:30794600-30811400	Weak transcription	Right Ventricle	heart
5	chr22:30794800-30811400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr22:30794800-30811600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr22:30794800-30818600	Weak transcription	Primary B cells from cord blood	blood
8	chr22:30795000-30814600	Weak transcription	Colon Smooth Muscle	Colon
9	chr22:30795200-30811600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr22:30795200-30814400	Weak transcription	Small Intestine	intestine
11	chr22:30795400-30812000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr22:30796000-30813400	Weak transcription	Fetal Kidney	kidney
13	chr22:30796200-30811400	Weak transcription	Placenta	Placenta
14	chr22:30797800-30816400	Strong transcription	Dnd41	blood
15	chr22:30798600-30811400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr22:30798600-30811600	Weak transcription	GM12878-XiMat	blood
17	chr22:30798600-30812000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr22:30798600-30812200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr22:30798800-30811400	Weak transcription	Colonic Mucosa	Colon
20	chr22:30799400-30812000	Weak transcription	Stomach Mucosa	stomach
21	chr22:30799400-30817600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr22:30800200-30812600	Genic enhancers	Muscle Satellite Cultured Cells	--
23	chr22:30800600-30811600	Weak transcription	Psoas Muscle	Psoas
24	chr22:30801200-30814400	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr22:30801400-30816600	Strong transcription	Fetal Stomach	stomach
26	chr22:30802000-30816400	Strong transcription	Stomach Smooth Muscle	stomach
27	chr22:30802200-30816200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr22:30802200-30817000	Genic enhancers	Liver	Liver
29	chr22:30802400-30811600	Strong transcription	Fetal Intestine Small	intestine
30	chr22:30802400-30811800	Strong transcription	Duodenum Mucosa	Duodenum
31	chr22:30802600-30811400	Weak transcription	Adipose Nuclei	Adipose
32	chr22:30802600-30811800	Strong transcription	Fetal Intestine Large	intestine
33	chr22:30802600-30814800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr22:30803200-30814000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr22:30803200-30817200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr22:30803400-30811600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr22:30803400-30815200	Strong transcription	Brain Substantia Nigra	brain
38	chr22:30803600-30811400	Weak transcription	Spleen	Spleen
39	chr22:30803600-30812000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr22:30804800-30815600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr22:30805000-30811600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr22:30805000-30811600	Weak transcription	Aorta	Aorta
43	chr22:30805000-30818200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr22:30805200-30811400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr22:30805200-30811600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr22:30805200-30811600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr22:30805200-30811600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr22:30805200-30812200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr22:30805200-30812200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr22:30805200-30816400	Weak transcription	NHDF-Ad	bronchial

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