Variant report

Variant	rs1282461
Chromosome Location	chr11:74576421-74576422
allele	A/G
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	chr11:74575505-74577153	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:74575902-74576953	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:74576381-74576624	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74459747..74461427-chr11:74574531..74576961,2	MCF-7	breast:
2	chr11:74575930..74578650-chr11:74579963..74582889,3	K562	blood:

Variant related genes	Relation type
XRRA1	TF binding region
ENSG00000166439	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11236269	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11605604	0.85[ASN][1000 genomes]
rs12363224	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1282460	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1282689	0.83[ASN][1000 genomes]
rs1282690	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1282695	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1292895	0.83[ASN][1000 genomes]
rs1297319	0.81[ASN][1000 genomes]
rs1303525	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1315297	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1583342	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2028343	0.81[ASN][1000 genomes]
rs2028344	0.81[ASN][1000 genomes]
rs2033532	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs41531051	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs471462	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs473080	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs473256	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs480840	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs483615	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs495246	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs497772	0.84[AFR][1000 genomes]
rs502225	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs505688	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs508319	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs511021	0.81[ASN][1000 genomes]
rs511890	0.81[ASN][1000 genomes]
rs512780	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs513137	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs519741	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs527529	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs529249	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs529488	0.81[ASN][1000 genomes]
rs538502	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs543244	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs546643	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs550491	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs550869	0.81[ASN][1000 genomes]
rs550980	0.83[ASN][1000 genomes]
rs557483	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs561589	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs562265	0.83[ASN][1000 genomes]
rs565767	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs567956	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs568558	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs568758	0.81[ASN][1000 genomes]
rs571446	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs573925	0.85[ASN][1000 genomes]
rs577102	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs580142	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs590105	0.85[ASN][1000 genomes]
rs599722	0.82[AMR][1000 genomes]
rs603062	0.85[ASN][1000 genomes]
rs614832	0.83[ASN][1000 genomes]
rs616085	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs625268	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs629573	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs641584	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs643807	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs646287	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs688665	0.83[ASN][1000 genomes]
rs9444	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs997465	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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
rs1282461	XRRA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74552800-74576800	Strong transcription	Stomach Smooth Muscle	stomach
2	chr11:74562200-74595800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:74563400-74576600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr11:74564800-74576600	Weak transcription	NH-A	brain
5	chr11:74569800-74577200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:74569800-74588400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr11:74570000-74577000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
8	chr11:74570000-74588400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:74570600-74578800	ZNF genes & repeats	Fetal Brain Female	brain
10	chr11:74570600-74585600	ZNF genes & repeats	Dnd41	blood
11	chr11:74570600-74588400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
12	chr11:74570800-74576800	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr11:74570800-74578800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:74570800-74579400	ZNF genes & repeats	Fetal Intestine Small	intestine
15	chr11:74570800-74579800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr11:74570800-74584800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr11:74571000-74588400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
18	chr11:74571200-74577000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:74571200-74584400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr11:74571200-74585200	ZNF genes & repeats	Brain Germinal Matrix	brain
21	chr11:74571600-74578600	ZNF genes & repeats	Fetal Muscle Leg	muscle
22	chr11:74572200-74576800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr11:74572200-74577000	Strong transcription	HepG2	liver
24	chr11:74572400-74576600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:74572400-74576600	Strong transcription	Pancreatic Islets	Pancreatic Islet
26	chr11:74572400-74576800	Strong transcription	Left Ventricle	heart
27	chr11:74573000-74576800	Weak transcription	Psoas Muscle	Psoas
28	chr11:74573200-74578200	ZNF genes & repeats	Aorta	Aorta
29	chr11:74573600-74579600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:74573600-74588400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:74574000-74578200	ZNF genes & repeats	Esophagus	oesophagus
32	chr11:74574200-74577200	ZNF genes & repeats	Ovary	ovary
33	chr11:74574200-74588400	ZNF genes & repeats	Adipose Nuclei	Adipose
34	chr11:74574400-74576600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr11:74574400-74576600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr11:74574800-74576600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr11:74574800-74576600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr11:74574800-74576600	Weak transcription	NHEK	skin
39	chr11:74574800-74576800	Strong transcription	Right Ventricle	heart
40	chr11:74574800-74576800	Weak transcription	HMEC	breast
41	chr11:74574800-74577000	ZNF genes & repeats	Spleen	Spleen
42	chr11:74574800-74577200	ZNF genes & repeats	Lung	lung
43	chr11:74574800-74577600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
44	chr11:74574800-74586600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
45	chr11:74575000-74576600	Weak transcription	HUVEC	blood vessel
46	chr11:74575000-74579400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
47	chr11:74575200-74576600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr11:74575400-74577200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
49	chr11:74575400-74577600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
50	chr11:74575400-74578200	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--

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