Variant report

Variant	rs8143159
Chromosome Location	chr22:31671882-31671883
allele	C/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	chr22:31667497..31670495-chr22:31671096..31674566,4	K562	blood:
2	chr22:31671882..31673528-chr22:31684555..31686967,2	K562	blood:
3	chr22:31670705..31674081-chr22:31684491..31687873,4	MCF-7	breast:
4	chr22:31670909..31673998-chr22:31741262..31743913,3	MCF-7	breast:
5	chr22:31671882..31674678-chr22:31684555..31687561,3	K562	blood:
6	chr22:31635531..31637522-chr22:31669683..31672388,2	MCF-7	breast:
7	chr22:31671853..31673887-chr22:31677470..31679780,2	MCF-7	breast:
8	chr22:31670893..31672907-chr22:31673053..31674567,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000182541	Chromatin interaction
ENSG00000100105	Chromatin interaction
ENSG00000100100	Chromatin interaction
ENSG00000213888	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1034587	0.82[MEX][hapmap]
rs11089493	0.87[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs11089495	0.83[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11089496	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1123705	0.81[CEU][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1138706	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11556237	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11703576	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11704156	1.00[CHD][hapmap];0.86[MEX][hapmap]
rs11704523	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12157877	0.86[CEU][hapmap];0.85[YRI][hapmap]
rs16989459	1.00[CHD][hapmap];0.86[MEX][hapmap]
rs16989469	0.87[CEU][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985726	0.86[AMR][1000 genomes]
rs2057951	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs2899161	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs3091392	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs4293639	0.81[EUR][1000 genomes]
rs4820972	1.00[CHD][hapmap];0.86[MEX][hapmap]
rs55837074	0.88[EUR][1000 genomes]
rs56292834	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5749231	0.82[MEX][hapmap]
rs57523999	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5753523	0.88[EUR][1000 genomes]
rs5994386	0.81[EUR][1000 genomes]
rs5994387	0.81[EUR][1000 genomes]
rs5997917	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997921	0.81[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs5997924	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997930	0.82[ASW][hapmap];0.87[LWK][hapmap]
rs5997937	0.83[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap]
rs5997942	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5997948	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5997956	0.81[EUR][1000 genomes]
rs5997959	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs5997965	0.81[EUR][1000 genomes]
rs695455	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs695630	0.80[EUR][1000 genomes]
rs695682	1.00[CEU][hapmap]
rs713619	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs7285027	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7285716	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7286926	0.87[CEU][hapmap]
rs7287715	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs738658	0.92[GIH][hapmap];0.87[MEX][hapmap]
rs739428	0.87[CEU][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8595	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459871	chr22:31551160-31680624	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	nsv588893	chr22:31551160-31680624	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1067003	chr22:31558663-31697093	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1058844	chr22:31597104-31725296	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv3375680	chr22:31671802-31673700	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8143159	SFI1	cis	cerebellum	SCAN
rs8143159	DUSP18	cis	cerebellum	SCAN
rs8143159	DUSP18	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31645000-31677600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr22:31650200-31675600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr22:31650200-31679200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr22:31650600-31676400	Weak transcription	Hela-S3	cervix
5	chr22:31651800-31675800	Strong transcription	HMEC	breast
6	chr22:31652800-31675800	Strong transcription	NHEK	skin
7	chr22:31652800-31679400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr22:31653800-31676200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr22:31654000-31676400	Strong transcription	Thymus	Thymus
10	chr22:31654000-31680400	Strong transcription	Lung	lung
11	chr22:31654000-31685600	Strong transcription	Fetal Stomach	stomach
12	chr22:31654200-31677200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:31654200-31680200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr22:31654200-31680400	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr22:31654400-31679600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr22:31655400-31680800	Weak transcription	K562	blood
17	chr22:31656800-31674000	Weak transcription	Brain Angular Gyrus	brain
18	chr22:31657800-31681200	Strong transcription	Adipose Nuclei	Adipose
19	chr22:31659000-31685600	Weak transcription	Psoas Muscle	Psoas
20	chr22:31659400-31678600	Strong transcription	Fetal Muscle Leg	muscle
21	chr22:31661400-31677800	Weak transcription	A549	lung
22	chr22:31661600-31673800	Strong transcription	Fetal Thymus	thymus
23	chr22:31661600-31674200	Strong transcription	Liver	Liver
24	chr22:31661800-31677000	Strong transcription	Spleen	Spleen
25	chr22:31661800-31677600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr22:31663800-31673000	Genic enhancers	Placenta	Placenta
27	chr22:31665600-31679400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr22:31665800-31678800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr22:31666000-31682600	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr22:31666000-31684200	Strong transcription	Aorta	Aorta
31	chr22:31666200-31675200	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr22:31667000-31676200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr22:31667000-31676400	Strong transcription	Fetal Lung	lung
34	chr22:31667000-31684600	Weak transcription	Right Atrium	heart
35	chr22:31667200-31672200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr22:31667400-31672400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr22:31667400-31676800	Strong transcription	Osteobl	bone
38	chr22:31667400-31677200	Strong transcription	Dnd41	blood
39	chr22:31667600-31672000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr22:31667800-31672000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
41	chr22:31667800-31672000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
42	chr22:31668000-31673400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr22:31668000-31675000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr22:31668400-31674000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr22:31668400-31681200	Strong transcription	NHLF	lung
46	chr22:31668600-31674400	Strong transcription	NHDF-Ad	bronchial
47	chr22:31668800-31675400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr22:31668800-31680400	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr22:31669000-31672400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr22:31669000-31672400	Strong transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links