Variant report

Variant	rs625268
Chromosome Location	chr11:74563742-74563743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:74563639-74563776	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:74555484..74559559-chr11:74563409..74567288,4	K562	blood:
2	chr11:74551525..74553766-chr11:74563114..74564936,2	K562	blood:
3	chr11:74563617..74565503-chr11:74581945..74584615,2	K562	blood:
4	chr11:74559768..74561678-chr11:74563525..74565103,2	K562	blood:

Variant related genes	Relation type
XRRA1	TF binding region
ENSG00000242999	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11236269	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11605604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12363224	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1282460	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1282461	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1282689	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1282690	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1282692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs1282695	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1292895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1297319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1303525	0.81[AMR][1000 genomes]
rs1315297	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1583342	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2028343	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2028344	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2033532	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2919057	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs41531051	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4245439	0.84[CEU][hapmap];0.88[JPT][hapmap]
rs471462	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs473080	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs473256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs480840	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs483615	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4944945	0.92[YRI][hapmap]
rs495246	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs497772	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs502225	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs505688	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs508319	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs511021	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs511890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs512780	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs513137	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs519741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs527529	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs529249	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs529488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs537054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs538502	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs543244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs546643	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs550491	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs550869	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs550980	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs557483	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs561589	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs562265	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs565767	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs567956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs568558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs568758	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs571446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs573925	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs577063	0.86[EUR][1000 genomes]
rs577102	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs580142	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs590105	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs599722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs603062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs614832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs616085	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs624786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs629573	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs641584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs643807	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs646287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs688665	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9444	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs997465	0.86[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv897916	chr11:74465068-74574677	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv897917	chr11:74474266-74595507	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs625268	XRRA1	cis	Adipose Subcutaneous	GTEx
rs625268	XRRA1	cis	Whole Blood	GTEx
rs625268	XRRA1	cis	Artery Tibial	GTEx
rs625268	XRRA1	cis	Esophagus Mucosa	GTEx
rs625268	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs625268	RP11-147I3.1	cis	Thyroid	GTEx
rs625268	XRRA1	cis	Muscle Skeletal	GTEx
rs625268	XRRA1	cis	lung	GTEx
rs625268	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs625268	XRRA1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74528000-74576400	Weak transcription	Stomach Mucosa	stomach
2	chr11:74543800-74565800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:74544200-74570800	Strong transcription	Duodenum Mucosa	Duodenum
4	chr11:74545600-74564600	Strong transcription	Fetal Muscle Trunk	muscle
5	chr11:74545600-74568400	Strong transcription	Fetal Intestine Large	intestine
6	chr11:74545800-74565000	Strong transcription	Fetal Muscle Leg	muscle
7	chr11:74546000-74566800	Strong transcription	Fetal Stomach	stomach
8	chr11:74547600-74571400	Weak transcription	Fetal Brain Male	brain
9	chr11:74549400-74567600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:74550600-74564600	Strong transcription	Fetal Intestine Small	intestine
11	chr11:74551000-74568400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr11:74552600-74565400	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr11:74552800-74576800	Strong transcription	Stomach Smooth Muscle	stomach
14	chr11:74553800-74569400	Weak transcription	Fetal Heart	heart
15	chr11:74554200-74567600	Weak transcription	Psoas Muscle	Psoas
16	chr11:74554800-74571600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:74555800-74569800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:74558200-74564400	Strong transcription	Thymus	Thymus
19	chr11:74558200-74564600	Strong transcription	Dnd41	blood
20	chr11:74558200-74565200	Strong transcription	Colonic Mucosa	Colon
21	chr11:74558400-74564000	Strong transcription	Fetal Brain Female	brain
22	chr11:74558400-74564200	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr11:74558400-74564600	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr11:74558600-74565000	Strong transcription	Primary T cells from cord blood	blood
25	chr11:74558600-74565800	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr11:74558800-74564600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:74558800-74565400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:74558800-74567400	Weak transcription	Small Intestine	intestine
29	chr11:74559000-74571400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr11:74559200-74565400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:74559200-74571400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr11:74559200-74571800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr11:74559400-74570000	Weak transcription	Right Ventricle	heart
34	chr11:74560200-74564800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr11:74560200-74569800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:74560400-74564000	Strong transcription	Brain Germinal Matrix	brain
37	chr11:74560400-74565400	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr11:74560600-74564800	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr11:74560600-74571200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr11:74560800-74564600	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr11:74561000-74564200	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr11:74561000-74564600	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr11:74561000-74567800	Weak transcription	Brain Angular Gyrus	brain
44	chr11:74561200-74564600	Strong transcription	Brain Cingulate Gyrus	brain
45	chr11:74561200-74571200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr11:74561400-74565200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:74561400-74568600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr11:74561600-74564000	Strong transcription	Esophagus	oesophagus
49	chr11:74561600-74564400	Strong transcription	GM12878-XiMat	blood
50	chr11:74561600-74565400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links