Variant report

Variant	rs10494535
Chromosome Location	chr1:180858459-180858460
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180855821..180859018-chr1:180875717..180879005,3	MCF-7	breast:
2	chr1:180857822..180860157-chr1:180861248..180863128,2	MCF-7	breast:
3	chr1:180857763..180859865-chr1:180868905..180871208,2	K562	blood:
4	chr1:180858397..180859188-chr1:180886465..180887001,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225857	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12401315	0.84[ASW][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs12404501	0.88[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs12408146	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12408176	0.84[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs12565658	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12566450	0.84[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16856367	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16856409	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16856422	0.81[ASN][1000 genomes]
rs17302054	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2271668	0.81[JPT][hapmap]
rs34451113	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4439326	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74135839	0.87[ASN][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	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10494535	RGS16	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180805800-180881000	Weak transcription	Aorta	Aorta
2	chr1:180812200-180867000	Weak transcription	Ovary	ovary
3	chr1:180822000-180862800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:180822800-180862800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:180823600-180860000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:180823800-180862600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:180824000-180867600	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:180824000-180880800	Weak transcription	Right Ventricle	heart
9	chr1:180828600-180867800	Weak transcription	HSMM	muscle
10	chr1:180830000-180867600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:180831200-180858600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:180832800-180861800	Weak transcription	HepG2	liver
13	chr1:180835400-180862800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:180835800-180858800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:180835800-180861600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:180835800-180870400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:180841000-180867800	Weak transcription	Lung	lung
18	chr1:180842200-180858600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:180843600-180862800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:180843800-180858600	Weak transcription	HMEC	breast
21	chr1:180844200-180872200	Weak transcription	Esophagus	oesophagus
22	chr1:180844400-180867400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:180845800-180869000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:180847400-180875400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:180849400-180867200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:180851000-180867000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:180851400-180867400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:180851400-180867600	Weak transcription	Fetal Heart	heart
29	chr1:180851600-180858600	Weak transcription	Fetal Brain Male	brain
30	chr1:180851600-180860200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:180851600-180862600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:180851600-180864200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:180851600-180867600	Weak transcription	Brain Germinal Matrix	brain
34	chr1:180851600-180867800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:180851800-180861600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:180851800-180867400	Weak transcription	Fetal Intestine Small	intestine
37	chr1:180852000-180870400	Weak transcription	A549	lung
38	chr1:180853600-180858600	Weak transcription	NHEK	skin
39	chr1:180853600-180862800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:180853600-180867200	Weak transcription	Adipose Nuclei	Adipose
41	chr1:180853800-180862800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:180853800-180867800	Weak transcription	Fetal Stomach	stomach
43	chr1:180854000-180866400	Weak transcription	Primary B cells from cord blood	blood
44	chr1:180854400-180862000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:180854400-180862000	Weak transcription	K562	blood
46	chr1:180854400-180862200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:180854400-180866800	Weak transcription	Left Ventricle	heart
48	chr1:180854800-180866800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:180855000-180862800	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr1:180856000-180859200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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