Variant report

Variant	rs10899052
Chromosome Location	chr11:74646213-74646214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74644656..74646769-chr11:74653647..74656340,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10160410	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10751241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10793105	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10793107	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10793108	0.91[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899045	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899053	0.91[CEU][hapmap];0.91[JPT][hapmap]
rs10899054	0.83[AMR][1000 genomes]
rs10899058	0.91[CEU][hapmap];0.91[JPT][hapmap]
rs11236244	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11236281	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs11236282	0.91[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes]
rs11236289	0.81[AMR][1000 genomes]
rs11236290	0.83[AMR][1000 genomes]
rs11236294	0.91[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs11603294	0.89[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes]
rs12221841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12223417	0.95[JPT][hapmap]
rs12225372	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12225387	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12419113	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12419929	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12421899	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12574850	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12575200	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12576129	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12577127	0.91[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes]
rs12577614	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1371410	0.91[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs17133461	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2119028	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2165162	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2165163	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2304683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3814726	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4245440	0.91[CEU][hapmap];0.95[JPT][hapmap]
rs4387374	0.91[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes]
rs4483614	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4944061	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4944950	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4944960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4944961	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4944963	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4944965	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4944968	0.83[AMR][1000 genomes]
rs56194145	0.84[AMR][1000 genomes]
rs59143825	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59328242	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61671395	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61734374	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61894779	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61894839	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7102619	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7103136	0.91[JPT][hapmap]
rs7105085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7128739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs725460	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7396866	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes]
rs7483351	0.90[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs7928381	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs919877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9787775	0.95[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9787897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	nsv832210	chr11:74562782-74732133	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs10899052	XRRA1	cis	lung	GTEx
rs10899052	XRRA1	cis	Muscle Skeletal	GTEx
rs10899052	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs10899052	XRRA1	cis	Heart Left Ventricle	GTEx
rs10899052	XRRA1	cis	Esophagus Mucosa	GTEx
rs10899052	RP11-147I3.1	cis	Esophagus Muscularis	GTEx
rs10899052	RP11-147I3.1	cis	Thyroid	GTEx
rs10899052	XRRA1	cis	Stomach	GTEx
rs10899052	XRRA1	cis	Thyroid	GTEx
rs10899052	XRRA1	cis	Esophagus Muscularis	GTEx
rs10899052	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs10899052	XRRA1	cis	lesional skin	skin_eQTL
rs10899052	XRRA1	cis	normal skin	skin_eQTL
rs10899052	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs10899052	XRRA1	cis	Nerve Tibial	GTEx
rs10899052	XRRA1	cis	Adipose Subcutaneous	GTEx
rs10899052	XRRA1	cis	Whole Blood	GTEx
rs10899052	XRRA1	cis	Artery Tibial	GTEx
rs10899052	XRRA1	cis	Artery Aorta	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74594800-74646600	Weak transcription	Small Intestine	intestine
2	chr11:74616400-74656200	Weak transcription	Stomach Mucosa	stomach
3	chr11:74617400-74648200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr11:74618000-74659600	Weak transcription	Esophagus	oesophagus
5	chr11:74618400-74653800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:74620400-74659600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr11:74627800-74659200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:74628200-74659600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:74630800-74659000	Weak transcription	Fetal Brain Male	brain
10	chr11:74631600-74659000	Weak transcription	Hela-S3	cervix
11	chr11:74632200-74659600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:74632400-74647200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:74632400-74647200	Weak transcription	Lung	lung
14	chr11:74632400-74648400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr11:74633000-74659400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:74634400-74646600	Weak transcription	Psoas Muscle	Psoas
17	chr11:74636000-74656200	Strong transcription	Fetal Intestine Large	intestine
18	chr11:74636000-74658200	Strong transcription	Fetal Muscle Trunk	muscle
19	chr11:74636800-74648000	Strong transcription	Stomach Smooth Muscle	stomach
20	chr11:74637400-74656400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr11:74637600-74646800	Weak transcription	GM12878-XiMat	blood
22	chr11:74637800-74655400	Strong transcription	Fetal Stomach	stomach
23	chr11:74638800-74648400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:74641200-74647200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:74641600-74659000	Weak transcription	A549	lung
26	chr11:74642000-74659400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:74642000-74659600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr11:74642200-74647400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr11:74642400-74656000	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr11:74642600-74656200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr11:74642800-74647400	Strong transcription	Brain Angular Gyrus	brain
32	chr11:74642800-74648200	Strong transcription	Adipose Nuclei	Adipose
33	chr11:74642800-74655600	Strong transcription	Placenta	Placenta
34	chr11:74643000-74649000	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr11:74643200-74648000	Strong transcription	Liver	Liver
36	chr11:74643200-74648200	Strong transcription	Fetal Muscle Leg	muscle
37	chr11:74643200-74648400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr11:74643200-74648600	Strong transcription	Colonic Mucosa	Colon
39	chr11:74643200-74649400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr11:74643200-74650000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr11:74643200-74650200	Strong transcription	HepG2	liver
42	chr11:74643200-74652200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:74643200-74653600	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr11:74643200-74653800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr11:74643400-74647800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:74643400-74647800	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr11:74643400-74648000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr11:74643400-74648000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:74643400-74648000	Strong transcription	Brain Anterior Caudate	brain
50	chr11:74643400-74648000	Strong transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links