Variant report

Variant	rs561604401
Chromosome Location	chr11:66887067-66887068
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	POLR2A	chr11:66886650-66887441	GM12892	blood:	n/a	n/a
2	HA-E2F1	chr11:66886325-66887381	Hela-S3	cervix:	n/a	chr11:66886354-66886368 chr11:66886699-66886708 chr11:66886761-66886771 chr11:66886552-66886561 chr11:66887262-66887271 chr11:66886387-66886396
3	TCF12	chr11:66886516-66887085	ECC-1	luminal epithelium:	n/a	n/a
4	RELA	chr11:66886461-66887799	GM12891	blood:	n/a	n/a
5	ETS1	chr11:66887054-66887323	K562	blood:	n/a	chr11:66887263-66887274 chr11:66887257-66887268
6	YY1	chr11:66886441-66887082	ECC-1	luminal epithelium:	n/a	chr11:66886754-66886762 chr11:66886748-66886767 chr11:66886743-66886765 chr11:66886755-66886765 chr11:66886747-66886767 chr11:66886753-66886765 chr11:66886755-66886765
7	ELF1	chr11:66887067-66887326	K562	blood:	n/a	chr11:66887275-66887287
8	YY1	chr11:66886287-66887488	GM12878	blood:	n/a	chr11:66886754-66886762 chr11:66887265-66887274 chr11:66886748-66886767 chr11:66886743-66886765 chr11:66886755-66886765 chr11:66886747-66886767 chr11:66886753-66886765 chr11:66886755-66886765
9	MAZ	chr11:66886245-66887735	Hela-S3	cervix:	n/a	chr11:66887263-66887273
10	YY1	chr11:66886265-66887420	K562	blood:	n/a	chr11:66886754-66886762 chr11:66887265-66887274 chr11:66886748-66886767 chr11:66886743-66886765 chr11:66886755-66886765 chr11:66886747-66886767 chr11:66886753-66886765 chr11:66886755-66886765
11	CTCFL	chr11:66887052-66887294	K562	blood:	n/a	n/a
12	REST	chr11:66886544-66887097	HL-60	blood:	n/a	chr11:66886843-66886851 chr11:66886613-66886626
13	YY1	chr11:66886450-66887304	GM12878	blood:	n/a	chr11:66886754-66886762 chr11:66887265-66887274 chr11:66886748-66886767 chr11:66886743-66886765 chr11:66886755-66886765 chr11:66886747-66886767 chr11:66886753-66886765 chr11:66886755-66886765
14	CTCF	chr11:66887052-66887288	HepG2	liver:	n/a	chr11:66887164-66887182 chr11:66887170-66887179
15	YY1	chr11:66886515-66887118	ECC-1	luminal epithelium:	n/a	chr11:66886754-66886762 chr11:66886748-66886767 chr11:66886743-66886765 chr11:66886755-66886765 chr11:66886747-66886767 chr11:66886753-66886765 chr11:66886755-66886765
16	MAZ	chr11:66885004-66887904	IMR90	lung:	n/a	chr11:66886120-66886129 chr11:66886002-66886011 chr11:66887263-66887273
17	CHD1	chr11:66886631-66887341	GM12878	blood:	n/a	n/a
18	POLR2A	chr11:66886140-66887322	Raji	blood:	n/a	n/a
19	YY1	chr11:66886469-66887304	GM12891	blood:	n/a	chr11:66886754-66886762 chr11:66887265-66887274 chr11:66886748-66886767 chr11:66886743-66886765 chr11:66886755-66886765 chr11:66886747-66886767 chr11:66886753-66886765 chr11:66886755-66886765
20	CTCF	chr11:66887060-66887210	NHEK	skin:	n/a	chr11:66887164-66887182 chr11:66887170-66887179
21	CTCF	chr11:66887000-66887150	NHLF	lung:	n/a	n/a
22	TAF1	chr11:66886474-66887085	H1-neurons	neurons:	n/a	n/a
23	ZBTB7A	chr11:66886026-66887546	ECC-1	luminal epithelium:	n/a	chr11:66887292-66887301 chr11:66887025-66887033
24	POLR2A	chr11:66885979-66887213	MCF-7	breast:	n/a	n/a
25	POLR2A	chr11:66886486-66887171	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr11:66886981-66887313	H1-hESC	embryonic stem cell:	n/a	chr11:66887164-66887182 chr11:66887170-66887179
27	TAF1	chr11:66886491-66887153	ECC-1	luminal epithelium:	n/a	n/a
28	SIN3AK20	chr11:66886404-66887511	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr11:66886308-66887669	K562	blood:	n/a	n/a
30	PAX5	chr11:66887047-66887320	GM12892	blood:	n/a	chr11:66887266-66887275
31	ZBTB7A	chr11:66885950-66887409	K562	blood:	n/a	chr11:66887292-66887301 chr11:66887025-66887033 chr11:66886008-66886015
32	POLR2A	chr11:66886491-66887196	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr11:66886285-66887129	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr11:66885165-66887278	GM18505	blood:	n/a	n/a
35	EGR1	chr11:66887065-66887418	K562	blood:	n/a	chr11:66887262-66887272 chr11:66887263-66887276
36	YY1	chr11:66886457-66887112	H1-hESC	embryonic stem cell:	n/a	chr11:66886754-66886762 chr11:66886748-66886767 chr11:66886743-66886765 chr11:66886755-66886765 chr11:66886747-66886767 chr11:66886753-66886765 chr11:66886755-66886765
37	POLR2A	chr11:66886280-66887171	ECC-1	luminal epithelium:	n/a	n/a
38	YY1	chr11:66886548-66887132	SK-N-SH_RA	brain:	n/a	chr11:66886754-66886762 chr11:66886748-66886767 chr11:66886743-66886765 chr11:66886755-66886765 chr11:66886747-66886767 chr11:66886753-66886765 chr11:66886755-66886765
39	POLR2A	chr11:66886471-66887123	SK-N-MC	brain:	n/a	n/a
40	MAZ	chr11:66885269-66887072	GM12878	blood:	n/a	chr11:66886120-66886129 chr11:66886002-66886011
41	POLR2A	chr11:66886584-66887085	K562	blood:	n/a	n/a
42	POLR2A	chr11:66886331-66887259	HepG2	liver:	n/a	n/a
43	CTCF	chr11:66887060-66887210	AG04449	skin:	n/a	chr11:66887164-66887182 chr11:66887170-66887179
44	POLR2A	chr11:66886249-66887289	A549	lung:	n/a	n/a
45	YY1	chr11:66886563-66887119	GM12891	blood:	n/a	chr11:66886754-66886762 chr11:66886748-66886767 chr11:66886743-66886765 chr11:66886755-66886765 chr11:66886747-66886767 chr11:66886753-66886765 chr11:66886755-66886765
46	SIN3A	chr11:66885690-66887976	H1-hESC	embryonic stem cell:	n/a	chr11:66886856-66886867 chr11:66886721-66886729
47	POLR2A	chr11:66886149-66887190	H1-neurons	neurons:	n/a	n/a
48	CTCF	chr11:66887060-66887210	SAEC	small airway:	n/a	chr11:66887164-66887182 chr11:66887170-66887179
49	POLR2A	chr11:66886489-66887067	ProgFib	skin:	n/a	n/a
50	UBTF	chr11:66886735-66888333	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:66885940..66887950-chr11:67395860..67397869,2	K562	blood:
2	chr11:66886805..66888356-chr20:52209357..52211197,2	MCF-7	breast:
3	chr11:66885437..66888305-chr11:67055921..67058495,2	MCF-7	breast:
4	chr11:66821625..66825972-chr11:66885437..66888104,7	MCF-7	breast:
5	chr11:66885002..66889173-chr11:67005085..67009324,11	K562	blood:
6	chr11:66884916..66890908-chr11:67005112..67010354,8	MCF-7	breast:
7	chr11:66886604..66887153-chr17:19551576..19552186,2	NB4	blood:
8	chr11:66886660..66888352-chr11:67075399..67077454,2	K562	blood:
9	chr11:66821404..66826403-chr11:66884710..66889541,16	MCF-7	breast:
10	chr11:66883623..66889678-chr11:67005085..67009894,16	K562	blood:

Variant related genes	Relation type
KDM2A	TF binding region
ENSG00000072210	Chromatin interaction
ENSG00000173156	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000172830	Chromatin interaction
ENSG00000173120	Chromatin interaction
ENSG00000167799	Chromatin interaction
ENSG00000172932	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv532287	chr11:66784014-67023899	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	esv3412807	chr11:66884326-66888124	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv3397435	chr11:66884601-66887149	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	esv3400268	chr11:66884676-66888099	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv3328460	chr11:66884901-66888249	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66884800-66888800	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr11:66884800-66889200	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr11:66885000-66887200	Weak transcription	Fetal Brain Male	brain
4	chr11:66885000-66888600	Active TSS	Brain Substantia Nigra	brain
5	chr11:66885000-66888800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:66885000-66888800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:66885000-66889000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:66885000-66889000	Active TSS	Lung	lung
9	chr11:66885000-66889000	Active TSS	Osteobl	bone
10	chr11:66885000-66889200	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr11:66885000-66889600	Active TSS	Psoas Muscle	Psoas
12	chr11:66885000-66889800	Active TSS	Fetal Brain Female	brain
13	chr11:66885000-66889800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr11:66885200-66887400	Weak transcription	Fetal Heart	heart
15	chr11:66885200-66887600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr11:66885200-66887800	Active TSS	Spleen	Spleen
17	chr11:66885200-66888000	Active TSS	Primary T cells from cord blood	blood
18	chr11:66885200-66888400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr11:66885200-66888400	Active TSS	Brain Cingulate Gyrus	brain
20	chr11:66885200-66888400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr11:66885200-66888600	Active TSS	Duodenum Mucosa	Duodenum
22	chr11:66885200-66888600	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr11:66885200-66888800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr11:66885200-66888800	Active TSS	Esophagus	oesophagus
25	chr11:66885200-66888800	Active TSS	Gastric	stomach
26	chr11:66885200-66889000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr11:66885200-66889000	Active TSS	H9 Cell Line	embryonic stem cell
28	chr11:66885200-66889000	Active TSS	Brain Angular Gyrus	brain
29	chr11:66885200-66889000	Active TSS	Colon Smooth Muscle	Colon
30	chr11:66885200-66889000	Active TSS	Placenta Amnion	Placenta Amnion
31	chr11:66885200-66889200	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr11:66885200-66889200	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr11:66885200-66889200	Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr11:66885200-66889400	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr11:66885200-66889400	Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr11:66885200-66889400	Active TSS	Brain Hippocampus Middle	brain
37	chr11:66885200-66889600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr11:66885200-66889600	Active TSS	Ovary	ovary
39	chr11:66885200-66889800	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr11:66885200-66889800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:66885200-66890000	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr11:66885200-66890000	Active TSS	HSMM	muscle
43	chr11:66885200-66890400	Active TSS	Brain Germinal Matrix	brain
44	chr11:66885200-66890600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:66885400-66887200	Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr11:66885400-66887400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr11:66885400-66887600	Active TSS	Primary B cells from cord blood	blood
48	chr11:66885400-66887600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr11:66885400-66887800	Active TSS	Primary B cells from peripheral blood	blood
50	chr11:66885400-66888000	Active TSS	Primary monocytes fromperipheralblood	blood

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