Variant report

Variant	rs7287402
Chromosome Location	chr22:31654823-31654824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:31654802-31654833	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31642310..31646378-chr22:31653276..31655946,3	MCF-7	breast:
2	chr22:31643031..31646502-chr22:31653237..31655706,4	MCF-7	breast:

Variant related genes	Relation type
LIMK2	TF binding region
ENSG00000182541	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11703927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166373	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12167361	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13056815	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13057841	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs131200	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs131202	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs131209	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs131213	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs131219	0.89[EUR][1000 genomes]
rs140074	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs140077	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2009132	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012451	0.81[MEX][hapmap];0.80[TSI][hapmap]
rs2013254	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2027982	0.91[MEX][hapmap]
rs2413048	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28523714	0.84[EUR][1000 genomes]
rs28715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28716	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28813120	0.95[EUR][1000 genomes]
rs34873968	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4820045	0.93[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs4820961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820969	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5753558	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5753576	0.89[EUR][1000 genomes]
rs5994376	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs5994397	0.93[CEU][hapmap]
rs5997887	0.81[EUR][1000 genomes]
rs5997898	0.87[MEX][hapmap]
rs5997900	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5997909	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997919	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997929	1.00[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];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997932	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997938	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5997960	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5997971	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs6518737	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs6518745	0.93[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs713947	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7285171	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7286648	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap]
rs7288643	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7288735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7289189	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7289337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs739427	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8141987	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8143002	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs878718	0.84[GIH][hapmap];0.85[MKK][hapmap]
rs926928	0.92[CEU][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs9606835	0.86[EUR][1000 genomes]
rs9609263	0.86[MEX][hapmap]
rs9619169	0.81[EUR][1000 genomes]
rs9619187	0.96[EUR][1000 genomes]
rs9621216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9621221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9621227	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7287402	SFI1	cis	cerebellum	SCAN
rs7287402	SFI1	cis	Thyroid	GTEx
rs7287402	LIMK2	cis	cerebellum	SCAN
rs7287402	PISD	cis	cerebellum	SCAN
rs7287402	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs7287402	CRYBB1	cis	cerebellum	SCAN
rs7287402	MN1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31644200-31665800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr22:31644600-31658000	Weak transcription	Psoas Muscle	Psoas
3	chr22:31644600-31668600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr22:31645000-31668400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr22:31645000-31668600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr22:31645000-31677600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr22:31645200-31667000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr22:31645400-31661800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr22:31646600-31655400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr22:31646800-31655000	Weak transcription	Aorta	Aorta
11	chr22:31647200-31655000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr22:31650000-31655200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr22:31650200-31655000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr22:31650200-31666200	Strong transcription	HepG2	liver
15	chr22:31650200-31675600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr22:31650200-31679200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr22:31650400-31658000	Weak transcription	Small Intestine	intestine
18	chr22:31650400-31660600	Strong transcription	Fetal Intestine Large	intestine
19	chr22:31650600-31655000	Weak transcription	Right Ventricle	heart
20	chr22:31650600-31656800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr22:31650600-31676400	Weak transcription	Hela-S3	cervix
22	chr22:31651400-31670200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr22:31651600-31667000	Weak transcription	Fetal Heart	heart
24	chr22:31651800-31675800	Strong transcription	HMEC	breast
25	chr22:31652800-31659800	Strong transcription	Fetal Intestine Small	intestine
26	chr22:31652800-31675800	Strong transcription	NHEK	skin
27	chr22:31652800-31679400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr22:31653000-31657200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr22:31653000-31657800	Strong transcription	Placenta	Placenta
30	chr22:31653000-31667400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr22:31653400-31670200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr22:31653600-31660800	Strong transcription	Fetal Thymus	thymus
33	chr22:31653600-31665000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr22:31653600-31668400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr22:31653800-31665000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr22:31653800-31667800	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr22:31653800-31668600	Weak transcription	Fetal Brain Male	brain
38	chr22:31653800-31670800	Strong transcription	Primary T cells from cord blood	blood
39	chr22:31653800-31676200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr22:31654000-31655000	Strong transcription	Gastric	stomach
41	chr22:31654000-31655800	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr22:31654000-31656600	Strong transcription	Colonic Mucosa	Colon
43	chr22:31654000-31657200	Strong transcription	Fetal Muscle Leg	muscle
44	chr22:31654000-31657400	Strong transcription	HSMMtube	muscle
45	chr22:31654000-31659000	Strong transcription	Duodenum Mucosa	Duodenum
46	chr22:31654000-31660400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr22:31654000-31660600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr22:31654000-31660600	Strong transcription	Primary B cells from cord blood	blood
49	chr22:31654000-31660600	Strong transcription	Dnd41	blood
50	chr22:31654000-31660800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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