Variant report

Variant	rs10489210
Chromosome Location	chr1:168312854-168312855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:168300197..168302893-chr1:168310234..168313350,3	K562	blood:
2	chr1:168312661..168313699-chr1:168334688..168335805,3	K562	blood:
3	chr1:168311615..168313900-chr1:168348090..168350975,2	MCF-7	breast:
4	chr1:168300197..168303468-chr1:168311046..168313350,3	K562	blood:
5	chr1:168312525..168314328-chr1:168315876..168317472,2	K562	blood:
6	chr1:168311820..168313033-chr1:168408760..168409687,3	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10800356	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10918873	0.97[ASN][1000 genomes]
rs12034832	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12123087	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12128782	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12136596	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137679	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12403490	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12409703	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12566982	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1569467	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16860447	0.88[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs1977060	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2268556	0.89[ASN][1000 genomes]
rs2268557	0.88[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs2268559	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2268560	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2900726	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4656583	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6427127	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6670176	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6697421	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7532903	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555108	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760685	0.88[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.90[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	nsv831825	chr1:168179175-168353062	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1002007	chr1:168179463-168375973	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10489210	RGS5	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168310600-168313000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:168310600-168313000	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr1:168311200-168313200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:168311600-168313000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr1:168311600-168313000	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr1:168311600-168313000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr1:168311600-168313800	Enhancers	Placenta Amnion	Placenta Amnion
8	chr1:168311600-168314200	Enhancers	Colon Smooth Muscle	Colon
9	chr1:168311800-168313400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr1:168311800-168313600	Enhancers	Fetal Brain Female	brain
11	chr1:168311800-168314200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:168312000-168313000	Weak transcription	Aorta	Aorta
13	chr1:168312000-168313600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:168312000-168313600	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr1:168312000-168313800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:168312000-168317200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:168312000-168317600	Weak transcription	Psoas Muscle	Psoas
18	chr1:168312000-168317800	Weak transcription	Left Ventricle	heart
19	chr1:168312200-168318000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:168312200-168318200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:168312200-168318200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:168312400-168313000	Enhancers	Ovary	ovary
23	chr1:168312400-168313200	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr1:168312400-168313200	Enhancers	Brain Anterior Caudate	brain
25	chr1:168312400-168313200	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr1:168312400-168313200	Enhancers	Brain Substantia Nigra	brain
27	chr1:168312400-168313400	Enhancers	Brain Angular Gyrus	brain
28	chr1:168312400-168314000	Enhancers	Brain Cingulate Gyrus	brain
29	chr1:168312400-168314200	Enhancers	Liver	Liver
30	chr1:168312400-168314400	Enhancers	Fetal Brain Male	brain
31	chr1:168312400-168317200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:168312400-168317200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr1:168312400-168317400	Weak transcription	Primary B cells from cord blood	blood
34	chr1:168312400-168318200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:168312600-168313000	Enhancers	Brain Hippocampus Middle	brain
36	chr1:168312600-168313200	Enhancers	HepG2	liver
37	chr1:168312600-168317200	Weak transcription	Primary T cells from cord blood	blood
38	chr1:168312600-168317400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:168312600-168317400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:168312800-168313000	Enhancers	Stomach Smooth Muscle	stomach
41	chr1:168312800-168313000	Enhancers	Spleen	Spleen
42	chr1:168312800-168317000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:168312800-168317000	Weak transcription	Dnd41	blood
44	chr1:168312800-168317200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:168312800-168317200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:168312800-168317200	Weak transcription	K562	blood
47	chr1:168312800-168317800	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links