Variant report

Variant	rs948562
Chromosome Location	chr11:58347765-58347766
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	chr11:58342402-58348892	K562	blood:	n/a	n/a
2	RUNX3	chr11:58347723-58348110	GM12878	blood:	n/a	n/a
3	MXI1	chr11:58344695-58348006	GM12878	blood:	n/a	n/a
4	MYC	chr11:58344556-58348161	K562	blood:	n/a	chr11:58346672-58346682 chr11:58346577-58346587 chr11:58346587-58346597
5	POLR2A	chr11:58344454-58347997	MCF10A-Er-Src	breast:	n/a	n/a
6	NFIC	chr11:58346599-58348245	GM12878	blood:	n/a	n/a
7	CHD1	chr11:58346700-58347832	GM12878	blood:	n/a	n/a
8	MXI1	chr11:58347011-58347916	K562	blood:	n/a	n/a
9	POLR2A	chr11:58344753-58347803	HepG2	liver:	n/a	n/a
10	POLR2A	chr11:58341968-58347772	GM12892	blood:	n/a	n/a
11	POLR2A	chr11:58344885-58347765	H1-hESC	embryonic stem cell:	n/a	n/a
12	IRF1	chr11:58347049-58347817	K562	blood:	n/a	chr11:58347575-58347587 chr11:58347576-58347586 chr11:58347572-58347586
13	MTA3	chr11:58346883-58348018	GM12878	blood:	n/a	n/a
14	ATF2	chr11:58347715-58348202	GM12878	blood:	n/a	n/a
15	FOXM1	chr11:58347659-58348148	GM12878	blood:	n/a	n/a
16	MXI1	chr11:58344356-58348358	SK-N-SH	brain:	n/a	n/a
17	ATF2	chr11:58347706-58348152	GM12878	blood:	n/a	n/a
18	MAX	chr11:58345032-58347898	Hela-S3	cervix:	n/a	chr11:58346672-58346682 chr11:58346577-58346587 chr11:58346587-58346597
19	FOXM1	chr11:58344440-58347992	GM12878	blood:	n/a	chr11:58344711-58344719
20	POLR2A	chr11:58343765-58347822	GM12878	blood:	n/a	n/a
21	POLR2A	chr11:58344243-58347833	Hela-S3	cervix:	n/a	n/a
22	MAZ	chr11:58344276-58347813	IMR90	lung:	n/a	chr11:58346672-58346682 chr11:58346577-58346587 chr11:58346587-58346597
23	ARID3A	chr11:58346978-58347892	K562	blood:	n/a	n/a
24	POLR2A	chr11:58340757-58348164	GM12891	blood:	n/a	n/a
25	CHD1	chr11:58344203-58348469	IMR90	lung:	n/a	chr11:58346265-58346274 chr11:58346484-58346494 chr11:58346341-58346350 chr11:58346680-58346690
26	CHD1	chr11:58346724-58347839	H1-hESC	embryonic stem cell:	n/a	n/a
27	HCFC1	chr11:58344165-58348252	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr11:58344271-58347875	K562	blood:	n/a	n/a
29	POLR2A	chr11:58342626-58348333	IMR90	lung:	n/a	n/a
30	MXI1	chr11:58344266-58348057	IMR90	lung:	n/a	n/a
31	SIN3A	chr11:58344502-58347778	H1-hESC	embryonic stem cell:	n/a	n/a
32	REST	chr11:58344918-58347935	H1-neurons	neurons:	n/a	chr11:58346278-58346291
33	BATF	chr11:58347727-58348174	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:58345286..58347963-chr11:58389614..58393452,3	MCF-7	breast:
2	chr11:58347130..58349444-chr11:58352908..58354763,3	MCF-7	breast:
3	chr11:57434798..57437115-chr11:58345701..58348083,4	MCF-7	breast:
4	chr11:57433251..57435131-chr11:58346916..58348765,2	K562	blood:
5	chr11:58346682..58349272-chr11:58349301..58352571,4	MCF-7	breast:
6	chr11:57433251..57437103-chr11:58344962..58348416,5	K562	blood:
7	chr11:57297015..57298977-chr11:58345779..58348496,3	K562	blood:
8	chr11:57423476..57425127-chr11:58344978..58347964,2	K562	blood:
9	chr11:58343669..58348848-chr11:58387112..58391418,8	K562	blood:
10	chr11:58345131..58348848-chr11:58387112..58390850,4	K562	blood:

Variant related genes	Relation type
LPXN	TF binding region
ENSG00000134809	Chromatin interaction
ENSG00000242689	Chromatin interaction
ENSG00000172409	Chromatin interaction
ENSG00000156599	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11229438	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[TSI][hapmap];0.94[ASN][1000 genomes]
rs11229439	0.91[ASN][1000 genomes]
rs11229440	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap]
rs11229479	0.94[ASN][1000 genomes]
rs11229532	1.00[ASN][1000 genomes]
rs11229535	1.00[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]
rs11229537	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229544	1.00[ASN][1000 genomes]
rs11229552	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11541682	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12361887	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12365551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17473544	0.92[ASN][1000 genomes]
rs17489568	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17568220	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1800169	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1938601	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1944051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2186381	0.95[EUR][1000 genomes]
rs2298607	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60767173	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60998298	0.97[ASN][1000 genomes]
rs7112350	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73470773	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73470778	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7481388	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7482383	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7484263	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7945889	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv528190	chr11:58336620-58347765	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
3	esv3400270	chr11:58345401-58348249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Lymphoma	23349640	GWAS catalog

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58343800-58347800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr11:58344000-58347800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr11:58344200-58348200	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr11:58344400-58347800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:58344400-58347800	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr11:58344400-58347800	Active TSS	Aorta	Aorta
7	chr11:58344400-58348000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr11:58344400-58348000	Active TSS	H9 Cell Line	embryonic stem cell
9	chr11:58344400-58348000	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr11:58344400-58348000	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr11:58344400-58348200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:58344400-58348400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:58344400-58349200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr11:58344400-58349400	Active TSS	K562	blood
15	chr11:58344600-58347800	Active TSS	Brain Cingulate Gyrus	brain
16	chr11:58344600-58348000	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr11:58344600-58348000	Active TSS	Brain Angular Gyrus	brain
18	chr11:58344600-58348000	Active TSS	Colonic Mucosa	Colon
19	chr11:58344600-58348000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr11:58344600-58348000	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr11:58344600-58348000	Active TSS	HSMM	muscle
22	chr11:58344600-58348000	Active TSS	NHDF-Ad	bronchial
23	chr11:58344600-58348200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr11:58344600-58348200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:58344600-58348200	Active TSS	Fetal Intestine Small	intestine
26	chr11:58344600-58348400	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr11:58344600-58348400	Active TSS	NHLF	lung
28	chr11:58344600-58348600	Active TSS	Psoas Muscle	Psoas
29	chr11:58344600-58348800	Active TSS	GM12878-XiMat	blood
30	chr11:58344600-58349000	Active TSS	H1 Cell Line	embryonic stem cell
31	chr11:58344600-58349000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:58344600-58350000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:58344800-58347800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr11:58344800-58347800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:58344800-58347800	Active TSS	Dnd41	blood
36	chr11:58344800-58348000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr11:58344800-58348200	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr11:58344800-58348200	Active TSS	A549	lung
39	chr11:58344800-58348400	Active TSS	Right Ventricle	heart
40	chr11:58344800-58348600	Active TSS	Fetal Intestine Large	intestine
41	chr11:58344800-58348800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr11:58345000-58347800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:58345000-58347800	Active TSS	Liver	Liver
44	chr11:58345000-58347800	Active TSS	Fetal Heart	heart
45	chr11:58345000-58347800	Active TSS	Fetal Kidney	kidney
46	chr11:58345000-58347800	Active TSS	Fetal Lung	lung
47	chr11:58345000-58348000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr11:58345000-58348000	Active TSS	Brain Hippocampus Middle	brain
49	chr11:58345000-58348000	Active TSS	Stomach Smooth Muscle	stomach
50	chr11:58345000-58348000	Active TSS	Osteobl	bone

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