Variant report

Variant	rs4899161
Chromosome Location	chr14:65540901-65540902
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:65540391..65543232-chr14:65544493..65546797,2	K562	blood:
2	chr14:65535365..65536995-chr14:65539588..65541589,2	K562	blood:
3	chr14:65539049..65542312-chr14:65547524..65550100,3	K562	blood:
4	chr14:65530728..65534685-chr14:65538811..65541539,3	K562	blood:

Variant related genes	Relation type
ENSG00000259118	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10143198	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs10151162	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs10873180	0.83[ASN][1000 genomes]
rs10873181	0.83[ASN][1000 genomes]
rs10873182	0.83[ASN][1000 genomes]
rs10873183	0.83[ASN][1000 genomes]
rs10873185	0.80[ASN][1000 genomes]
rs11158572	0.85[EUR][1000 genomes]
rs11158573	0.85[EUR][1000 genomes]
rs11158574	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs11158577	0.80[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs11158578	0.83[ASN][1000 genomes]
rs1124751	0.92[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs1124752	0.92[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs11623603	0.81[ASN][1000 genomes]
rs11625045	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs11626720	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12147959	0.84[EUR][1000 genomes]
rs1256417	0.92[EUR][1000 genomes]
rs1270074	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs1271582	0.92[CEU][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs12880781	0.92[CEU][hapmap];0.84[CHB][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs12887607	0.87[CEU][hapmap]
rs12888794	0.85[EUR][1000 genomes]
rs17102423	0.81[ASN][1000 genomes]
rs17825846	0.83[CEU][hapmap]
rs1953228	0.90[EUR][1000 genomes]
rs1953232	0.92[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs1957948	0.92[CEU][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs1957949	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs1998688	0.92[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs2093989	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2151755	0.81[CEU][hapmap]
rs2763888	0.86[EUR][1000 genomes]
rs2781373	0.92[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs2781374	0.89[EUR][1000 genomes]
rs35769504	0.85[EUR][1000 genomes]
rs45604339	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4902357	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs4902358	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4902359	0.83[CEU][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs4902360	0.92[CEU][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs4902361	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs4902363	0.81[ASN][1000 genomes]
rs55658675	0.90[EUR][1000 genomes]
rs61987428	0.83[ASN][1000 genomes]
rs61987429	0.83[ASN][1000 genomes]
rs7143495	0.92[CEU][hapmap];0.84[CHB][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs7150646	0.83[CEU][hapmap];0.91[EUR][1000 genomes]
rs7154852	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7156617	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];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7159443	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs7161394	0.92[CEU][hapmap];0.84[CHB][hapmap];0.90[EUR][1000 genomes]
rs762810	0.92[MEX][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8004805	0.82[CHB][hapmap]
rs8009396	0.80[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs8009714	0.85[EUR][1000 genomes]
rs8010213	0.92[EUR][1000 genomes]
rs8018788	0.81[ASN][1000 genomes]
rs8181937	0.87[EUR][1000 genomes]
rs8181938	0.87[EUR][1000 genomes]
rs8181939	0.91[CEU][hapmap];0.83[CHB][hapmap];0.90[EUR][1000 genomes]
rs868814	0.84[CHB][hapmap];0.85[MEX][hapmap]
rs884683	0.91[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs942626	0.92[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs942627	0.92[CEU][hapmap];0.84[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs942628	0.92[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs942629	0.81[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs998247	0.81[CEU][hapmap];0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832816	chr14:65473244-65644645	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4899161	GPX2	cis	cerebellum	SCAN
rs4899161	SIX4	cis	cerebellum	SCAN
rs4899161	WDR89	cis	cerebellum	SCAN
rs4899161	MAX	cis	cerebellum	SCAN
rs4899161	MAX	cis	parietal	SCAN
rs4899161	RAB15	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65471200-65546200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr14:65501800-65543200	Weak transcription	Fetal Brain Male	brain
3	chr14:65508600-65542000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr14:65527600-65545600	Strong transcription	Primary T cells from cord blood	blood
5	chr14:65527800-65553600	Strong transcription	Dnd41	blood
6	chr14:65528800-65555400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr14:65529600-65541600	Weak transcription	NH-A	brain
8	chr14:65529800-65543000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr14:65530000-65553000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr14:65530400-65543200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr14:65531200-65541400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr14:65532600-65542400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr14:65533200-65541200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr14:65533200-65541600	Weak transcription	Hela-S3	cervix
15	chr14:65533200-65542000	Weak transcription	A549	lung
16	chr14:65533400-65542200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr14:65534000-65553600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr14:65534400-65542200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr14:65534600-65546000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr14:65534800-65553400	Strong transcription	Thymus	Thymus
21	chr14:65535400-65541600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr14:65535600-65545600	Strong transcription	Fetal Stomach	stomach
23	chr14:65535600-65547000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr14:65536000-65553600	Strong transcription	Fetal Thymus	thymus
25	chr14:65536200-65541800	Enhancers	Fetal Heart	heart
26	chr14:65536200-65541800	Genic enhancers	Fetal Muscle Leg	muscle
27	chr14:65536600-65543200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr14:65536800-65541200	Weak transcription	Aorta	Aorta
29	chr14:65536800-65542800	Weak transcription	Fetal Lung	lung
30	chr14:65537000-65541200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr14:65537000-65541600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr14:65537000-65542400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr14:65537400-65542200	Enhancers	Right Ventricle	heart
34	chr14:65537600-65541800	Genic enhancers	Fetal Intestine Small	intestine
35	chr14:65537600-65542800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr14:65537600-65543200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr14:65537800-65541800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr14:65537800-65541800	Enhancers	Small Intestine	intestine
39	chr14:65537800-65542200	Enhancers	Stomach Mucosa	stomach
40	chr14:65537800-65542200	Weak transcription	HMEC	breast
41	chr14:65537800-65542600	Weak transcription	Brain Hippocampus Middle	brain
42	chr14:65538200-65541800	Enhancers	Adipose Nuclei	Adipose
43	chr14:65538200-65542600	Enhancers	Right Atrium	heart
44	chr14:65538200-65544600	Strong transcription	HSMM	muscle
45	chr14:65538400-65541200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr14:65538400-65541800	Enhancers	Esophagus	oesophagus
47	chr14:65538400-65542000	Genic enhancers	Fetal Intestine Large	intestine
48	chr14:65538400-65542600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
49	chr14:65538400-65545000	Strong transcription	GM12878-XiMat	blood
50	chr14:65538400-65545600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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