Variant report

Variant	rs590601
Chromosome Location	chr11:65149872-65149873
allele	A/C
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	IKZF1	chr11:65149378-65150349	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:65149178-65150505	ECC-1	luminal epithelium:	n/a	n/a
3	CTCF	chr11:65149751-65149979	GM10248	blood:	n/a	chr11:65149877-65149895 chr11:65149880-65149889
4	RAD21	chr11:65149753-65150089	H1-hESC	embryonic stem cell:	n/a	chr11:65149878-65149897
5	POLR2A	chr11:65149199-65150488	HUVEC	blood vessel:	n/a	n/a
6	YY1	chr11:65149215-65150522	A549	lung:	n/a	chr11:65149782-65149796
7	RUNX3	chr11:65149208-65150638	GM12878	blood:	n/a	n/a
8	HDAC2	chr11:65149359-65150375	K562	blood:	n/a	n/a
9	CTCF	chr11:65149705-65150065	K562	blood:	n/a	chr11:65149877-65149895 chr11:65149880-65149889
10	ZNF263	chr11:65149174-65150545	HEK293-T-REx	kidney:	n/a	chr11:65150039-65150048 chr11:65149305-65149314 chr11:65149927-65149936
11	EBF1	chr11:65149276-65150715	GM12878	blood:	n/a	chr11:65150045-65150054 chr11:65150043-65150056 chr11:65150044-65150055 chr11:65150045-65150055
12	TBL1XR1	chr11:65149285-65150315	GM12878	blood:	n/a	n/a
13	ELF1	chr11:65149804-65150250	K562	blood:	n/a	n/a
14	GTF2B	chr11:65149521-65150051	K562	blood:	n/a	n/a
15	RFX5	chr11:65149782-65150059	GM12878	blood:	n/a	n/a
16	YY1	chr11:65149578-65150185	GM12892	blood:	n/a	chr11:65149782-65149796
17	CTCF	chr11:65149780-65149930	GM12870	blood:	n/a	chr11:65149877-65149895 chr11:65149880-65149889
18	CTCF	chr11:65149721-65150062	T-47D	breast:	n/a	chr11:65149877-65149895 chr11:65149880-65149889
19	CTCF	chr11:65149800-65149950	NHEK	skin:	n/a	chr11:65149877-65149895 chr11:65149880-65149889
20	POLR2A	chr11:65149545-65150554	SK-N-SH	brain:	n/a	n/a
21	REST	chr11:65149112-65150600	A549	lung:	n/a	chr11:65149858-65149868
22	CHD1	chr11:65149556-65150403	GM12878	blood:	n/a	n/a
23	STAT3	chr11:65149303-65150058	MCF10A-Er-Src	breast:	n/a	chr11:65149426-65149446 chr11:65149923-65149935
24	CTCF	chr11:65149798-65149936	GM20000	blood:	n/a	chr11:65149877-65149895 chr11:65149880-65149889
25	JUND	chr11:65149333-65150485	MCF-7	breast:	n/a	chr11:65149948-65149957 chr11:65149951-65149959 chr11:65150007-65150019 chr11:65150005-65150016 chr11:65149946-65149958 chr11:65150009-65150017 chr11:65149946-65149957
26	CEBPD	chr11:65149350-65150415	HepG2	liver:	n/a	n/a
27	PAX5	chr11:65149133-65150647	GM12878	blood:	n/a	n/a
28	SIN3A	chr11:65149511-65150303	GM12878	blood:	n/a	chr11:65149791-65149804
29	NR2F2	chr11:65149146-65150714	K562	blood:	n/a	n/a
30	FOXA1	chr11:65149792-65150158	T-47D	breast:	n/a	n/a
31	CTCF	chr11:65149760-65149910	Hela-S3	cervix:	n/a	chr11:65149877-65149895 chr11:65149880-65149889
32	CTCF	chr11:65149800-65149950	SAEC	small airway:	n/a	chr11:65149877-65149895 chr11:65149880-65149889
33	HNF4A	chr11:65149169-65150018	HepG2	liver:	n/a	chr11:65149295-65149310
34	CTCF	chr11:65149740-65149890	HCM	heart:	n/a	chr11:65149880-65149889
35	RUNX3	chr11:65149123-65150639	GM12878	blood:	n/a	n/a
36	REST	chr11:65149745-65150112	SK-N-SH	brain:	n/a	chr11:65149858-65149868
37	MAFF	chr11:65149576-65150108	HepG2	liver:	n/a	chr11:65149755-65149773
38	FOS	chr11:65149691-65150191	K562	blood:	n/a	chr11:65149948-65149957 chr11:65149951-65149959 chr11:65150007-65150019 chr11:65150005-65150016 chr11:65149946-65149958 chr11:65150009-65150017 chr11:65149946-65149957
39	MAX	chr11:65149303-65150556	SK-N-SH	brain:	n/a	n/a
40	MAX	chr11:65149251-65150682	MCF-7	breast:	n/a	n/a
41	CTCF	chr11:65149800-65149950	AG04449	skin:	n/a	chr11:65149877-65149895 chr11:65149880-65149889
42	POLR2A	chr11:65149308-65150257	K562	blood:	n/a	n/a
43	POLR2A	chr11:65149058-65150875	GM12892	blood:	n/a	n/a
44	GABPA	chr11:65149208-65150068	Hela-S3	cervix:	n/a	n/a
45	BATF	chr11:65149733-65150318	GM12878	blood:	n/a	chr11:65150009-65150020
46	USF2	chr11:65149438-65150424	Hela-S3	cervix:	n/a	n/a
47	GATA2	chr11:65149256-65150352	HUVEC	blood vessel:	n/a	chr11:65149770-65149778 chr11:65150052-65150065 chr11:65150007-65150016 chr11:65149946-65149955 chr11:65149500-65149509 chr11:65150055-65150063 chr11:65149491-65149508
48	ZNF143	chr11:65149563-65150175	K562	blood:	n/a	chr11:65149915-65149934 chr11:65149986-65149995
49	CBX3	chr11:65149715-65150124	K562	blood:	n/a	n/a
50	JUND	chr11:65149282-65150323	K562	blood:	n/a	chr11:65149948-65149957 chr11:65149951-65149959 chr11:65150007-65150019 chr11:65150005-65150016 chr11:65149946-65149958 chr11:65150009-65150017 chr11:65149946-65149957

No.	Distal block	Cell Line	Cell type
1	chr11:65149482..65150810-chr11:65190165..65190760,3	Hela-S3	cervix:
2	chr11:65121664..65123613-chr11:65147869..65150112,2	MCF-7	breast:
3	chr1:249120467..249121137-chr11:65149363..65150092,2	Hela-S3	cervix:
4	chr11:65116402..65157784-chr11:65261420..65278410,154	K562	blood:
5	chr11:65098911..65102850-chr11:65147012..65151675,4	MCF-7	breast:
6	chr11:65081207..65084199-chr11:65149055..65151019,2	K562	blood:
7	chr11:64851366..64853197-chr11:65148381..65150307,2	MCF-7	breast:
8	chr11:65120584..65123151-chr11:65148447..65152021,3	K562	blood:
9	chr11:65148353..65151201-chr11:65310310..65312867,2	MCF-7	breast:
10	chr11:65148557..65151141-chr11:65342655..65344676,2	MCF-7	breast:

Variant related genes	Relation type
FRMD8	TF binding region
SLC25A45	TF binding region
ENSG00000133884	Chromatin interaction
ENSG00000149798	Chromatin interaction
ENSG00000173442	Chromatin interaction
ENSG00000264500	Chromatin interaction
ENSG00000175137	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000162300	Chromatin interaction
ENSG00000146670	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000168056	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000173825	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1194336	0.83[AMR][1000 genomes]
rs12795699	0.83[AMR][1000 genomes]
rs1784102	0.83[AMR][1000 genomes]
rs2957264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs472852	0.83[AMR][1000 genomes]
rs557777	1.00[AMR][1000 genomes]
rs624307	0.83[AMR][1000 genomes]
rs635411	0.85[AFR][1000 genomes]
rs683338	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
3	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
4	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
5	nsv541065	chr11:65117387-65271894	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	835 gene(s)	inside rSNPs	diseases
6	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	963 gene(s)	inside rSNPs	diseases
7	nsv897717	chr11:65140209-65278461	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	942 gene(s)	inside rSNPs	diseases
8	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
9	nsv541066	chr11:65142779-65271894	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	833 gene(s)	inside rSNPs	diseases
10	nsv541067	chr11:65142779-65313799	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	950 gene(s)	inside rSNPs	diseases
11	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
12	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
13	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
14	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65146200-65150800	Enhancers	Gastric	stomach
2	chr11:65147200-65150800	Flanking Active TSS	Duodenum Mucosa	Duodenum
3	chr11:65147800-65150800	Flanking Active TSS	Fetal Intestine Large	intestine
4	chr11:65148200-65153800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:65148400-65151000	Flanking Active TSS	Dnd41	blood
6	chr11:65148800-65150400	Active TSS	A549	lung
7	chr11:65148800-65150600	Flanking Active TSS	Fetal Intestine Small	intestine
8	chr11:65149000-65150400	Active TSS	Primary T cells from cord blood	blood
9	chr11:65149000-65150800	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr11:65149000-65151000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:65149000-65151000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:65149000-65151000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr11:65149200-65150200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:65149200-65150200	Active TSS	Right Ventricle	heart
15	chr11:65149200-65150400	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr11:65149200-65150400	Flanking Active TSS	Liver	Liver
17	chr11:65149200-65150400	Flanking Active TSS	Fetal Stomach	stomach
18	chr11:65149200-65150400	Active TSS	Psoas Muscle	Psoas
19	chr11:65149200-65150600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:65149200-65150600	Flanking Active TSS	Fetal Lung	lung
21	chr11:65149200-65150600	Flanking Active TSS	Fetal Muscle Leg	muscle
22	chr11:65149200-65150600	Flanking Active TSS	Fetal Thymus	thymus
23	chr11:65149200-65150600	Flanking Active TSS	K562	blood
24	chr11:65149200-65150800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr11:65149200-65150800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr11:65149200-65150800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr11:65149200-65150800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:65149200-65150800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:65149200-65150800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:65149200-65150800	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr11:65149200-65150800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:65149200-65151000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr11:65149200-65151000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr11:65149200-65151000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:65149200-65151000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr11:65149200-65151000	Flanking Active TSS	Rectal Smooth Muscle	rectum
37	chr11:65149200-65151000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr11:65149200-65151000	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr11:65149200-65151000	Flanking Active TSS	HSMM	muscle
40	chr11:65149400-65150000	Flanking Active TSS	Spleen	Spleen
41	chr11:65149400-65150000	Active TSS	Hela-S3	cervix
42	chr11:65149400-65150200	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr11:65149400-65150200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:65149400-65150200	Enhancers	Brain Germinal Matrix	brain
45	chr11:65149400-65150200	Active TSS	Right Atrium	heart
46	chr11:65149400-65150200	Active TSS	Small Intestine	intestine
47	chr11:65149400-65150400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr11:65149400-65150400	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr11:65149400-65150400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr11:65149400-65150400	Active TSS	Esophagus	oesophagus

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