Variant report

Variant	rs12419929
Chromosome Location	chr11:74611435-74611436
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10160410	0.89[ASN][1000 genomes]
rs10751241	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10793105	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10793107	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10793108	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899045	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899051	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899052	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899054	0.81[AMR][1000 genomes]
rs11236244	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11236282	0.81[AMR][1000 genomes]
rs11236290	0.81[AMR][1000 genomes]
rs11603294	0.81[AMR][1000 genomes]
rs12221841	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12225372	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12225387	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12419113	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12421899	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12574850	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12575200	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12576129	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12577127	0.81[AMR][1000 genomes]
rs12577614	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17133461	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2119028	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2165162	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2165163	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2298746	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2304683	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3814726	0.85[ASN][1000 genomes]
rs4387374	0.81[AMR][1000 genomes]
rs4483614	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4944061	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4944950	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4944960	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4944961	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4944963	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4944965	0.82[AMR][1000 genomes]
rs4944968	0.81[AMR][1000 genomes]
rs56194145	0.82[AMR][1000 genomes]
rs59143825	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59328242	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61671395	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61734374	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61894779	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61894839	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7102619	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7105085	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7128739	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs725460	0.85[AMR][1000 genomes]
rs7396866	0.82[AMR][1000 genomes]
rs7928381	0.84[ASN][1000 genomes]
rs919877	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9787775	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9787897	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[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	nsv932190	chr11:74359867-74618935	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
2	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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs12419929	XRRA1	cis	Nerve Tibial	GTEx
rs12419929	XRRA1	cis	lung	GTEx
rs12419929	XRRA1	cis	Artery Tibial	GTEx
rs12419929	XRRA1	cis	Esophagus Mucosa	GTEx
rs12419929	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs12419929	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs12419929	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs12419929	XRRA1	cis	Artery Aorta	GTEx
rs12419929	XRRA1	cis	Thyroid	GTEx
rs12419929	XRRA1	cis	Stomach	GTEx
rs12419929	RP11-147I3.1	cis	Esophagus Muscularis	GTEx
rs12419929	XRRA1	cis	Whole Blood	GTEx
rs12419929	XRRA1	cis	Muscle Skeletal	GTEx
rs12419929	XRRA1	cis	Adipose Subcutaneous	GTEx
rs12419929	XRRA1	cis	Esophagus Muscularis	GTEx
rs12419929	XRRA1	cis	Heart Left Ventricle	GTEx
rs12419929	RP11-147I3.1	cis	Thyroid	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74587400-74611800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr11:74587400-74629600	Weak transcription	Gastric	stomach
3	chr11:74588400-74630600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr11:74588400-74636000	Weak transcription	NHLF	lung
5	chr11:74594800-74646600	Weak transcription	Small Intestine	intestine
6	chr11:74595800-74611800	Weak transcription	Brain Angular Gyrus	brain
7	chr11:74596400-74612000	Weak transcription	HSMM	muscle
8	chr11:74596800-74619000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr11:74598200-74615200	Weak transcription	Osteobl	bone
10	chr11:74598400-74611800	Weak transcription	Dnd41	blood
11	chr11:74598400-74629600	Weak transcription	Colon Smooth Muscle	Colon
12	chr11:74599000-74611800	Weak transcription	Brain Hippocampus Middle	brain
13	chr11:74599200-74611600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr11:74599200-74619400	Weak transcription	Colonic Mucosa	Colon
15	chr11:74599400-74611800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:74603200-74617800	Weak transcription	K562	blood
17	chr11:74603800-74616600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr11:74605000-74611800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:74605600-74611600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:74606400-74611800	Weak transcription	Fetal Heart	heart
21	chr11:74606400-74612600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr11:74606600-74626400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr11:74606800-74616200	Weak transcription	NHEK	skin
24	chr11:74607000-74611600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:74607000-74611800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:74607200-74618000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr11:74607400-74613200	Weak transcription	Primary B cells from cord blood	blood
28	chr11:74607400-74617200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr11:74607600-74616400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr11:74607600-74616600	Weak transcription	Placenta	Placenta
31	chr11:74607600-74617200	Weak transcription	Thymus	Thymus
32	chr11:74607600-74618200	Weak transcription	Hela-S3	cervix
33	chr11:74607600-74637400	Weak transcription	Pancreas	Pancrea
34	chr11:74607800-74616200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:74607800-74616200	Weak transcription	Aorta	Aorta
36	chr11:74607800-74616400	Weak transcription	Primary T cells from cord blood	blood
37	chr11:74607800-74616400	Weak transcription	Left Ventricle	heart
38	chr11:74607800-74616400	Weak transcription	Lung	lung
39	chr11:74607800-74616600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:74607800-74618000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:74607800-74618000	Weak transcription	Ovary	ovary
42	chr11:74607800-74620800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr11:74608000-74611600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:74608000-74611600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr11:74608000-74611800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr11:74608000-74616600	Weak transcription	HepG2	liver
47	chr11:74608000-74618000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr11:74609400-74612000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr11:74609600-74612000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr11:74611000-74611600	ZNF genes & repeats	Fetal Intestine Small	intestine

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