Variant report

Variant	rs527529
Chromosome Location	chr11:74620800-74620801
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	NFIC	chr11:74620415-74620880	GM12878	blood:	n/a	n/a
2	MEF2C	chr11:74620316-74620863	GM12878	blood:	n/a	chr11:74620579-74620594 chr11:74620577-74620598 chr11:74620805-74620816 chr11:74620629-74620640 chr11:74620582-74620591 chr11:74620806-74620815 chr11:74620613-74620628 chr11:74620803-74620817 chr11:74620802-74620819 chr11:74620613-74620630 chr11:74620801-74620822 chr11:74620801-74620822 chr11:74620804-74620815
3	MEF2A	chr11:74620327-74620876	GM12878	blood:	n/a	chr11:74620579-74620594 chr11:74620577-74620598 chr11:74620805-74620816 chr11:74620629-74620640 chr11:74620582-74620591 chr11:74620806-74620815 chr11:74620613-74620628 chr11:74620803-74620817 chr11:74620802-74620819 chr11:74620613-74620630 chr11:74620801-74620822 chr11:74620801-74620822 chr11:74620804-74620815
4	MEF2A	chr11:74620316-74620862	GM12878	blood:	n/a	chr11:74620579-74620594 chr11:74620577-74620598 chr11:74620805-74620816 chr11:74620629-74620640 chr11:74620582-74620591 chr11:74620806-74620815 chr11:74620613-74620628 chr11:74620803-74620817 chr11:74620802-74620819 chr11:74620613-74620630 chr11:74620801-74620822 chr11:74620801-74620822 chr11:74620804-74620815

Variant related genes	Relation type
ENSG00000241170	TF binding region
XRRA1	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11236269	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605604	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12363224	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1282460	0.85[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]
rs1282461	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1282689	0.94[ASN][1000 genomes]
rs1282690	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1282692	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1282695	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1292895	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1297319	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1303525	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1315297	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1583342	0.85[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2028343	0.92[ASN][1000 genomes]
rs2028344	0.92[ASN][1000 genomes]
rs2033532	0.85[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes]
rs2919057	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs41531051	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4245439	0.88[JPT][hapmap]
rs471462	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs473080	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs473256	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480840	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483615	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4944945	0.92[YRI][hapmap]
rs495246	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs497772	0.80[AFR][1000 genomes]
rs502225	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs505688	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs508319	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs511021	0.92[ASN][1000 genomes]
rs511890	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs512780	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs513137	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs519741	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs529249	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529488	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs537054	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs538502	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs543244	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs546643	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs550491	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550869	0.92[ASN][1000 genomes]
rs550980	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs557483	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs561589	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs562265	0.94[ASN][1000 genomes]
rs565767	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs567956	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs568558	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];1.00[ASN][1000 genomes]
rs568758	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs571446	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs573925	1.00[ASN][1000 genomes]
rs577063	0.88[ASN][1000 genomes]
rs577102	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs580142	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs590105	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs599722	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs603062	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614832	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs616085	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs624786	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs625268	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]
rs629573	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs641584	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs643807	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs646287	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs688665	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9444	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs997465	0.86[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs527529	XRRA1	cis	Whole Blood	GTEx
rs527529	XRRA1	cis	Muscle Skeletal	GTEx
rs527529	XRRA1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74587400-74629600	Weak transcription	Gastric	stomach
2	chr11:74588400-74630600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr11:74588400-74636000	Weak transcription	NHLF	lung
4	chr11:74594800-74646600	Weak transcription	Small Intestine	intestine
5	chr11:74598400-74629600	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:74606600-74626400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr11:74607600-74637400	Weak transcription	Pancreas	Pancrea
8	chr11:74607800-74620800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr11:74612400-74629600	Weak transcription	NHDF-Ad	bronchial
10	chr11:74612800-74621200	Weak transcription	Fetal Kidney	kidney
11	chr11:74612800-74634000	Weak transcription	Psoas Muscle	Psoas
12	chr11:74613400-74621000	Weak transcription	Brain Substantia Nigra	brain
13	chr11:74613400-74632600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:74613600-74624000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr11:74613600-74627800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:74613800-74628600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:74613800-74637400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:74614200-74620800	Weak transcription	Brain Germinal Matrix	brain
19	chr11:74614400-74623000	Strong transcription	Fetal Intestine Small	intestine
20	chr11:74614600-74633600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr11:74615000-74629600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr11:74615000-74629600	Weak transcription	NH-A	brain
23	chr11:74615000-74636200	Weak transcription	A549	lung
24	chr11:74615200-74632600	Strong transcription	Liver	Liver
25	chr11:74615200-74637200	Weak transcription	HMEC	breast
26	chr11:74615400-74623600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:74615400-74626400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr11:74615600-74626600	Strong transcription	Dnd41	blood
29	chr11:74615800-74633600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:74615800-74644800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr11:74616000-74621200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr11:74616000-74622800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr11:74616000-74634200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr11:74616000-74634800	Strong transcription	Fetal Intestine Large	intestine
35	chr11:74616200-74626800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:74616200-74634000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr11:74616400-74621400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr11:74616400-74622200	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr11:74616400-74623600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr11:74616400-74633600	Strong transcription	Stomach Smooth Muscle	stomach
41	chr11:74616400-74634400	Strong transcription	Primary T cells from cord blood	blood
42	chr11:74616400-74646000	Weak transcription	Spleen	Spleen
43	chr11:74616400-74656200	Weak transcription	Stomach Mucosa	stomach
44	chr11:74616600-74622200	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr11:74616600-74622400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr11:74616600-74623200	Strong transcription	Adipose Nuclei	Adipose
47	chr11:74616600-74623400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr11:74616600-74629200	Weak transcription	Fetal Thymus	thymus
49	chr11:74616600-74632600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr11:74616600-74632600	Strong transcription	Rectal Mucosa Donor 29	rectum

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