Variant report

Variant	rs820830
Chromosome Location	chr5:74000130-74000131
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:73995760..73997460-chr5:73998842..74001561,2	K562	blood:
2	chr5:73979980..73983407-chr5:73996490..74001343,5	K562	blood:
3	chr5:73981038..73983852-chr5:73999852..74002635,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000049860	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10062244	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs1043968	0.82[JPT][hapmap]
rs10515189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10515190	0.84[YRI][hapmap]
rs10515191	0.83[JPT][hapmap]
rs1104272	0.82[ASN][1000 genomes]
rs11739122	0.83[JPT][hapmap]
rs11739301	0.83[JPT][hapmap]
rs11740871	0.90[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap]
rs11741464	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11741789	0.83[JPT][hapmap]
rs11742621	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11743415	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11743655	1.00[JPT][hapmap]
rs11746069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11746611	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11746717	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11746757	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11747965	0.82[JPT][hapmap]
rs11749137	0.83[JPT][hapmap]
rs11948188	0.83[JPT][hapmap]
rs11955898	0.83[JPT][hapmap]
rs1350097	0.83[JPT][hapmap]
rs1447453	0.83[JPT][hapmap]
rs1531103	0.90[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap]
rs16872340	0.83[ASW][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];0.84[YRI][hapmap]
rs16872346	0.83[JPT][hapmap]
rs17670605	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17670701	0.90[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs17670867	0.90[CEU][hapmap];0.90[CHB][hapmap]
rs17670897	0.90[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs17670975	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs17738111	0.90[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs17738266	0.89[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap]
rs17738565	0.90[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs17738645	0.90[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs17738674	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs17852781	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1979014	0.84[YRI][hapmap]
rs1992712	0.90[CEU][hapmap]
rs1993370	0.83[JPT][hapmap]
rs2044410	0.83[JPT][hapmap]
rs2061162	0.83[JPT][hapmap]
rs3733794	0.83[JPT][hapmap]
rs3932895	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3968877	0.90[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61093699	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62366366	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62366371	0.85[EUR][1000 genomes]
rs62366373	0.85[EUR][1000 genomes]
rs62366375	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62366376	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62366406	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6453075	0.91[JPT][hapmap]
rs6453081	0.83[ASW][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];0.84[YRI][hapmap]
rs6453084	0.83[JPT][hapmap]
rs6453086	0.83[JPT][hapmap]
rs6453087	0.82[JPT][hapmap]
rs6866082	0.83[JPT][hapmap]
rs6874609	0.83[JPT][hapmap]
rs6877116	0.82[JPT][hapmap]
rs6877442	0.83[JPT][hapmap]
rs6879781	0.81[JPT][hapmap]
rs6882499	0.83[JPT][hapmap]
rs6883061	0.83[JPT][hapmap]
rs6884843	0.83[JPT][hapmap]
rs6885675	0.88[JPT][hapmap]
rs6897698	0.83[JPT][hapmap]
rs72764640	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7728889	0.83[JPT][hapmap]
rs820825	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs820827	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820828	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs820832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs820834	0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs820835	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9686657	0.83[JPT][hapmap]

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	nsv598653	chr5:73992881-74095542	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs820830	NSA2	cis	cerebellum	SCAN
rs820830	NSA2	cis	parietal	SCAN
rs820830	GFM2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:73982000-74002200	Weak transcription	Fetal Brain Female	brain
2	chr5:73982000-74017400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:73982000-74061800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:73982200-74020600	Weak transcription	Fetal Brain Male	brain
5	chr5:73982400-74002200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:73983000-74001000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:73983000-74001600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:73983000-74017400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:73983000-74027000	Weak transcription	Fetal Heart	heart
10	chr5:73983200-74002200	Weak transcription	Esophagus	oesophagus
11	chr5:73983200-74030200	Weak transcription	Small Intestine	intestine
12	chr5:73983400-74016000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr5:73984400-74002200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr5:73984600-74000400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr5:73984600-74001000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:73984600-74001600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:73984600-74002600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr5:73985000-74002600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr5:73985200-74002600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:73987200-74017400	Weak transcription	Fetal Kidney	kidney
21	chr5:73987600-74014800	Weak transcription	Fetal Lung	lung
22	chr5:73988400-74021000	Weak transcription	Right Ventricle	heart
23	chr5:73989600-74001000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:73989800-74000600	Weak transcription	HUVEC	blood vessel
25	chr5:73989800-74002200	Weak transcription	Brain Angular Gyrus	brain
26	chr5:73989800-74002600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:73990000-74016200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr5:73990400-74013600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr5:73991400-74000800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:73991600-74002200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:73991800-74002400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:73992800-74000200	Strong transcription	Fetal Intestine Small	intestine
33	chr5:73993000-74001200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:73993000-74002200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:73993000-74002200	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr5:73993400-74014400	Weak transcription	Stomach Mucosa	stomach
37	chr5:73993400-74017400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr5:73993800-74001400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:73993800-74001600	Weak transcription	GM12878-XiMat	blood
40	chr5:73993800-74014600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr5:73993800-74014600	Weak transcription	HSMMtube	muscle
42	chr5:73993800-74019800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr5:73994000-74000400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr5:73994800-74000400	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr5:73995000-74001200	Weak transcription	NHDF-Ad	bronchial
46	chr5:73995000-74009800	Weak transcription	HMEC	breast
47	chr5:73995200-74001000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr5:73995400-74001000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr5:73995400-74002200	Weak transcription	Gastric	stomach
50	chr5:73995600-74001000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links