Variant report

Variant	rs888521
Chromosome Location	chr2:172218624-172218625
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	chr2:172218525..172220285-chr2:172222152..172224139,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10173812	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10195398	0.85[CHD][hapmap]
rs1125991	0.82[ASN][1000 genomes]
rs11674303	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11685308	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11695531	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1178014	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12327994	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12989804	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3731986	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731987	0.87[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs60545517	0.82[ASN][1000 genomes]
rs6744452	0.94[ASW][hapmap];0.82[CEU][hapmap];0.88[GIH][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7349355	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1003130	chr2:172189196-172237268	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs888521	WIPF1	cis	cerebellum	SCAN
rs888521	CDCA7	cis	cerebellum	SCAN
rs888521	SSB	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172172800-172222400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:172181000-172221600	Weak transcription	K562	blood
3	chr2:172204800-172222400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:172205000-172221400	Weak transcription	NHEK	skin
5	chr2:172205000-172221600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:172205000-172221800	Weak transcription	Osteobl	bone
7	chr2:172205000-172222400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:172205200-172221600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:172205200-172224000	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:172211000-172242600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:172212400-172221600	Weak transcription	HMEC	breast
12	chr2:172212400-172222400	Weak transcription	Aorta	Aorta
13	chr2:172212400-172231400	Weak transcription	Esophagus	oesophagus
14	chr2:172214200-172226000	Weak transcription	Left Ventricle	heart
15	chr2:172214400-172222400	Weak transcription	A549	lung
16	chr2:172214800-172218800	Weak transcription	Fetal Intestine Small	intestine
17	chr2:172214800-172221600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:172214800-172231600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:172215000-172222400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:172215000-172223000	Weak transcription	Fetal Stomach	stomach
21	chr2:172215400-172231800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:172215800-172231000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:172216000-172221400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:172216000-172222400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:172216400-172218800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:172216400-172222800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:172216400-172231400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr2:172216800-172221600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:172216800-172222000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:172217000-172219200	Weak transcription	Dnd41	blood
31	chr2:172217000-172220400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:172217000-172221600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:172217000-172224800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:172217200-172225000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:172217200-172231400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:172218200-172218800	Strong transcription	Primary B cells from cord blood	blood
37	chr2:172218200-172219000	Enhancers	HepG2	liver
38	chr2:172218400-172218800	Enhancers	H9 Cell Line	embryonic stem cell
39	chr2:172218400-172218800	Enhancers	Pancreas	Pancrea
40	chr2:172218400-172219000	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr2:172218400-172219000	ZNF genes & repeats	GM12878-XiMat	blood
42	chr2:172218600-172218800	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr2:172218600-172219000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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