Variant report

Variant	rs494474
Chromosome Location	chr11:74710217-74710218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74709588..74712387-chr11:74717812..74720338,3	K562	blood:
2	chr11:74699258..74701562-chr11:74709548..74713241,3	MCF-7	breast:
3	chr11:74704465..74706580-chr11:74709652..74711304,2	K562	blood:
4	chr11:74661075..74664022-chr11:74709710..74711926,2	K562	blood:
5	chr11:74709211..74711419-chr11:74713806..74715440,2	K562	blood:
6	chr11:74709502..74714442-chr11:74716351..74722182,6	K562	blood:

Variant related genes	Relation type
ENSG00000162139	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11236291	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11236292	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1125609	0.82[CEU][hapmap]
rs12287793	0.94[ASN][1000 genomes]
rs3018833	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs483271	0.81[JPT][hapmap]
rs487226	0.88[CEU][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs493001	0.88[CEU][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs4944962	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs500827	0.81[JPT][hapmap]
rs512782	0.81[JPT][hapmap]
rs514534	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs517666	0.82[CEU][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs522808	0.95[ASN][1000 genomes]
rs536412	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs544115	0.94[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs544891	0.81[JPT][hapmap];0.82[TSI][hapmap]
rs551371	0.92[ASN][1000 genomes]
rs559211	0.82[TSI][hapmap]
rs565377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566480	0.96[ASN][1000 genomes]
rs568310	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58778107	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58972415	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59860682	0.96[ASN][1000 genomes]
rs605954	0.82[CEU][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs629191	0.88[CEU][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs639768	0.94[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs650130	0.81[JPT][hapmap]
rs662062	0.81[JPT][hapmap];0.82[TSI][hapmap]
rs670246	0.88[CEU][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs671544	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs674122	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs681566	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs685116	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs693212	0.80[JPT][hapmap]
rs7128833	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7939123	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7952096	0.89[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7952209	0.94[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs494474	XRRA1	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74700400-74716400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:74700400-74723000	Weak transcription	Small Intestine	intestine
3	chr11:74700600-74716400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:74700600-74716400	Weak transcription	Aorta	Aorta
5	chr11:74700600-74716400	Weak transcription	Esophagus	oesophagus
6	chr11:74700600-74716400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:74700600-74716600	Weak transcription	Fetal Brain Male	brain
8	chr11:74700600-74722600	Weak transcription	HSMM	muscle
9	chr11:74700600-74725000	Weak transcription	HSMMtube	muscle
10	chr11:74700800-74716400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr11:74700800-74716400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr11:74700800-74716400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:74700800-74716400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr11:74700800-74716400	Weak transcription	NHLF	lung
15	chr11:74700800-74716600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:74701000-74716400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr11:74701000-74716400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr11:74701000-74716400	Weak transcription	Colonic Mucosa	Colon
19	chr11:74701000-74716600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:74701000-74716600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr11:74701000-74716600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr11:74701000-74716600	Weak transcription	Colon Smooth Muscle	Colon
23	chr11:74701000-74716600	Weak transcription	NH-A	brain
24	chr11:74701000-74722000	Weak transcription	Fetal Kidney	kidney
25	chr11:74701000-74722600	Weak transcription	HUVEC	blood vessel
26	chr11:74701000-74723800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr11:74701200-74716400	Weak transcription	A549	lung
28	chr11:74701400-74716400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr11:74701600-74721600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr11:74701800-74716600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr11:74702400-74716600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:74702400-74716600	Weak transcription	Fetal Heart	heart
33	chr11:74702400-74722800	Weak transcription	Stomach Mucosa	stomach
34	chr11:74702800-74716400	Weak transcription	Pancreas	Pancrea
35	chr11:74702800-74717600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr11:74703200-74720600	Weak transcription	Psoas Muscle	Psoas
37	chr11:74704800-74710800	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr11:74704800-74711200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr11:74705200-74710800	Strong transcription	Primary hematopoietic stem cells	blood
40	chr11:74705400-74710600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:74705400-74710800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr11:74705800-74716400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr11:74706000-74716600	Weak transcription	Brain Hippocampus Middle	brain
44	chr11:74706200-74716400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:74706400-74715400	Weak transcription	Hela-S3	cervix
46	chr11:74706400-74716400	Weak transcription	Brain Angular Gyrus	brain
47	chr11:74706400-74716400	Weak transcription	Fetal Brain Female	brain
48	chr11:74706400-74716400	Weak transcription	Gastric	stomach
49	chr11:74706400-74716400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr11:74706400-74716600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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