Variant report

Variant	rs616085
Chromosome Location	chr11:74661935-74661936
allele	G/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	CHD1	chr11:74661523-74662139	GM12878	blood:	n/a	n/a
2	PAX5	chr11:74661378-74662111	GM12878	blood:	n/a	chr11:74661621-74661640
3	PAX5	chr11:74661194-74662001	GM12892	blood:	n/a	chr11:74661621-74661640
4	PAX5	chr11:74661346-74662087	GM12878	blood:	n/a	chr11:74661621-74661640
5	PAX5	chr11:74661258-74662118	GM12878	blood:	n/a	chr11:74661621-74661640
6	POLR2A	chr11:74659666-74663417	GM12878	blood:	n/a	n/a
7	WRNIP1	chr11:74661562-74662229	GM12878	blood:	n/a	n/a
8	MTA3	chr11:74661292-74662579	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:74659778-74663158	GM18505	blood:	n/a	n/a
10	RELA	chr11:74659644-74661979	GM15510	blood:	n/a	n/a
11	POLR2A	chr11:74659565-74663285	GM12891	blood:	n/a	n/a
12	POLR2A	chr11:74659706-74662134	GM19099	blood:	n/a	n/a
13	POLR2A	chr11:74661894-74661947	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr11:74661096-74661963	HepG2	liver:	n/a	n/a
15	MXI1	chr11:74659380-74662170	SK-N-SH	brain:	n/a	n/a
16	MXI1	chr11:74659446-74662031	IMR90	lung:	n/a	n/a
17	POLR2A	chr11:74661425-74662141	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:74654949..74658411-chr11:74658805..74662988,5	MCF-7	breast:
2	chr11:74660462..74662157-chr11:74951131..74952954,2	K562	blood:
3	chr11:74658459..74662580-chr11:74698519..74701644,8	MCF-7	breast:
4	chr11:74661075..74664022-chr11:74709710..74711926,2	K562	blood:
5	chr11:74647283..74650920-chr11:74658326..74663032,5	K562	blood:

Variant related genes	Relation type
ENSG00000265344	TF binding region
XRRA1	TF binding region
ENSG00000162139	Chromatin interaction
ENSG00000261594	Chromatin interaction
ENSG00000166435	Chromatin interaction
ENSG00000265344	Chromatin interaction
ENSG00000255136	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11236269	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11605604	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12363224	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1282460	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1282461	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1282689	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1282690	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1282692	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1282695	0.98[ASN][1000 genomes]
rs1292895	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1297319	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1315297	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1583342	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2028343	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2028344	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2033532	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2851136	0.83[ASN][1000 genomes]
rs2919057	0.83[ASN][1000 genomes]
rs41531051	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs471462	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs473080	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs473256	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs480840	0.94[ASN][1000 genomes]
rs495246	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs502225	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs508319	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs511021	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs511890	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs513137	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs519741	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs527529	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs529249	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs529488	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs537054	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs538502	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs543244	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546643	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550491	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs550869	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550980	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs557483	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs562265	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567956	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568558	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs568758	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs571446	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs573925	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs577063	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs580142	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs590105	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs599722	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs603062	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs614832	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624786	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs625268	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs629573	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641584	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643807	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646287	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs688665	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs997465	0.84[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs616085	XRRA1	cis	Thyroid	GTEx
rs616085	RP11-147I3.1	cis	Thyroid	GTEx
rs616085	XRRA1	cis	lung	GTEx
rs616085	XRRA1	cis	Artery Tibial	GTEx
rs616085	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs616085	XRRA1	cis	Muscle Skeletal	GTEx
rs616085	XRRA1	cis	Whole Blood	GTEx
rs616085	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs616085	XRRA1	cis	Esophagus Mucosa	GTEx
rs616085	XRRA1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74659200-74662200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr11:74659400-74662000	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr11:74659400-74662200	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr11:74659400-74662200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:74659400-74662400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr11:74660600-74662200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr11:74660600-74662400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:74660600-74663000	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr11:74660800-74662000	Flanking Active TSS	Brain Germinal Matrix	brain
10	chr11:74660800-74662000	Flanking Active TSS	Fetal Brain Female	brain
11	chr11:74660800-74662200	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr11:74660800-74662400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:74660800-74662400	Flanking Active TSS	Liver	Liver
14	chr11:74660800-74662400	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr11:74660800-74662400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr11:74661000-74662000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:74661000-74662000	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr11:74661000-74662000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:74661000-74662000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr11:74661000-74662000	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr11:74661000-74662000	Flanking Active TSS	HUVEC	blood vessel
22	chr11:74661000-74662000	Flanking Active TSS	Osteobl	bone
23	chr11:74661000-74662200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr11:74661000-74662200	Flanking Active TSS	Hela-S3	cervix
25	chr11:74661000-74662800	Flanking Active TSS	Primary B cells from peripheral blood	blood
26	chr11:74661200-74662000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:74661200-74662000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:74661200-74662000	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr11:74661200-74662000	Transcr. at gene 5' and 3'	HepG2	liver
30	chr11:74661200-74662200	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr11:74661200-74662200	Flanking Active TSS	HMEC	breast
32	chr11:74661200-74662400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr11:74661200-74662600	Enhancers	Small Intestine	intestine
34	chr11:74661200-74662800	Enhancers	Spleen	Spleen
35	chr11:74661200-74665400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:74661200-74688600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr11:74661400-74662000	Enhancers	Fetal Intestine Small	intestine
38	chr11:74661400-74662000	Enhancers	Placenta	Placenta
39	chr11:74661400-74662200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:74661400-74662200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr11:74661400-74662200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr11:74661400-74662200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:74661400-74662200	Enhancers	Brain Substantia Nigra	brain
44	chr11:74661400-74662200	Enhancers	Esophagus	oesophagus
45	chr11:74661400-74662200	Enhancers	Gastric	stomach
46	chr11:74661400-74662200	Flanking Active TSS	Right Ventricle	heart
47	chr11:74661400-74662400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr11:74661400-74662400	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr11:74661400-74662600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr11:74661400-74662600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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