Variant report

Variant	rs59143825
Chromosome Location	chr11:74599594-74599595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10160410	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10751241	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10793105	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10793107	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10793108	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10899045	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10899051	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10899052	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10899054	0.81[AMR][1000 genomes]
rs11236244	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11236282	0.81[AMR][1000 genomes]
rs11236290	0.81[AMR][1000 genomes]
rs11603294	0.81[AMR][1000 genomes]
rs12221841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12225372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12225387	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12419113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12419929	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12421899	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12574850	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12575200	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12576129	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12577127	0.81[AMR][1000 genomes]
rs12577614	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17133461	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2119028	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2165162	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2165163	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2298746	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2304683	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3814726	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4387374	0.81[AMR][1000 genomes]
rs4483614	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4944061	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4944950	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4944960	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944961	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4944963	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4944965	0.82[AMR][1000 genomes]
rs4944968	0.81[AMR][1000 genomes]
rs56194145	0.82[AMR][1000 genomes]
rs59328242	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61671395	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61734374	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61894779	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61894839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7102619	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7105085	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7128739	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs725460	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7396866	0.82[AMR][1000 genomes]
rs7928381	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs919877	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9787775	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9787897	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59143825	XRRA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74586400-74604800	Weak transcription	Fetal Heart	heart
2	chr11:74587000-74600400	Weak transcription	HUVEC	blood vessel
3	chr11:74587400-74611800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr11:74587400-74629600	Weak transcription	Gastric	stomach
5	chr11:74588400-74601800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr11:74588400-74605400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr11:74588400-74606200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr11:74588400-74630600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr11:74588400-74636000	Weak transcription	NHLF	lung
10	chr11:74591800-74606000	Weak transcription	Right Ventricle	heart
11	chr11:74594400-74600000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr11:74594400-74600000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr11:74594600-74599600	ZNF genes & repeats	Fetal Muscle Leg	muscle
14	chr11:74594800-74646600	Weak transcription	Small Intestine	intestine
15	chr11:74595600-74606600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr11:74595800-74605200	Weak transcription	Brain Anterior Caudate	brain
17	chr11:74595800-74611800	Weak transcription	Brain Angular Gyrus	brain
18	chr11:74596200-74599800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr11:74596200-74605000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr11:74596200-74606200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr11:74596400-74606200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr11:74596400-74612000	Weak transcription	HSMM	muscle
23	chr11:74596800-74604800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr11:74596800-74619000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:74597200-74599800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
26	chr11:74597600-74599600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:74597600-74606200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:74598000-74600800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr11:74598000-74603000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr11:74598000-74606600	Weak transcription	Psoas Muscle	Psoas
31	chr11:74598000-74606800	Weak transcription	Left Ventricle	heart
32	chr11:74598200-74604600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr11:74598200-74604800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:74598200-74606200	Weak transcription	NHEK	skin
35	chr11:74598200-74609800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:74598200-74615200	Weak transcription	Osteobl	bone
37	chr11:74598400-74599600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr11:74598400-74599800	ZNF genes & repeats	Fetal Intestine Small	intestine
39	chr11:74598400-74604600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr11:74598400-74606200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:74598400-74606400	Weak transcription	Primary B cells from cord blood	blood
42	chr11:74598400-74611800	Weak transcription	Dnd41	blood
43	chr11:74598400-74629600	Weak transcription	Colon Smooth Muscle	Colon
44	chr11:74598600-74599600	ZNF genes & repeats	Fetal Stomach	stomach
45	chr11:74598600-74599600	ZNF genes & repeats	Lung	lung
46	chr11:74598600-74599600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr11:74598800-74607400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr11:74599000-74605000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr11:74599000-74606200	Weak transcription	Thymus	Thymus
50	chr11:74599000-74606800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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