Variant report

Variant	rs541244650
Chromosome Location	chr11:66886610-66886611
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	YY1	chr11:66886573-66887061	K562	blood:	n/a	chr11:66886754-66886762 chr11:66886748-66886767 chr11:66886743-66886765 chr11:66886755-66886765 chr11:66886747-66886767 chr11:66886753-66886765 chr11:66886755-66886765
2	POLR2A	chr11:66886291-66886747	H1-hESC	embryonic stem cell:	n/a	n/a
3	TCF3	chr11:66885670-66886759	GM12878	blood:	n/a	n/a
4	CHD2	chr11:66886031-66886946	GM12878	blood:	n/a	chr11:66886392-66886402
5	RCOR1	chr11:66886482-66886657	HepG2	liver:	n/a	n/a
6	SIN3AK20	chr11:66886509-66886859	PFSK-1	brain:	n/a	n/a
7	PML	chr11:66886577-66887013	MCF-7	breast:	n/a	n/a
8	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
9	TCF12	chr11:66886516-66887085	ECC-1	luminal epithelium:	n/a	n/a
10	RFX5	chr11:66886489-66886683	GM12878	blood:	n/a	n/a
11	SIN3AK20	chr11:66886506-66886655	HepG2	liver:	n/a	n/a
12	MXI1	chr11:66886414-66886938	GM12878	blood:	n/a	n/a
13	EGR1	chr11:66886185-66886993	ECC-1	luminal epithelium:	n/a	chr11:66886553-66886562 chr11:66886655-66886668 chr11:66886275-66886288 chr11:66886552-66886561 chr11:66886595-66886604 chr11:66886596-66886605 chr11:66886439-66886453 chr11:66886654-66886669 chr11:66886699-66886708 chr11:66886387-66886396 chr11:66886355-66886365
14	ELF1	chr11:66886468-66886738	K562	blood:	n/a	n/a
15	RELA	chr11:66886461-66887799	GM12891	blood:	n/a	n/a
16	FOXA2	chr11:66886271-66886869	A549	lung:	n/a	n/a
17	YY1	chr11:66886566-66886988	NT2-D1	testis:	n/a	chr11:66886754-66886762 chr11:66886748-66886767 chr11:66886743-66886765 chr11:66886755-66886765 chr11:66886747-66886767 chr11:66886753-66886765 chr11:66886755-66886765
18	MAZ	chr11:66886215-66886798	HepG2	liver:	n/a	n/a
19	CTCF	chr11:66886347-66886621	K562	blood:	n/a	n/a
20	CTCF	chr11:66886415-66886646	Spleen_OC	spleen:	n/a	n/a
21	CHD2	chr11:66886093-66886960	Hela-S3	cervix:	n/a	chr11:66886392-66886402
22	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
23	CREB1	chr11:66886172-66886870	H1-hESC	embryonic stem cell:	n/a	n/a
24	YY1	chr11:66886554-66887031	GM12892	blood:	n/a	chr11:66886754-66886762 chr11:66886748-66886767 chr11:66886743-66886765 chr11:66886755-66886765 chr11:66886747-66886767 chr11:66886753-66886765 chr11:66886755-66886765
25	TAF1	chr11:66886550-66887018	PFSK-1	brain:	n/a	n/a
26	MAX	chr11:66886012-66886862	MCF-7	breast:	n/a	chr11:66886120-66886129
27	REST	chr11:66886589-66887014	A549	lung:	n/a	chr11:66886843-66886851 chr11:66886613-66886626
28	POLR2A	chr11:66886471-66886991	K562	blood:	n/a	n/a
29	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
30	POLR2A	chr11:66885108-66886634	GM12892	blood:	n/a	n/a
31	TBP	chr11:66886509-66886907	H1-hESC	embryonic stem cell:	n/a	n/a
32	RCOR1	chr11:66886457-66886935	GM12878	blood:	n/a	n/a
33	MAZ	chr11:66886245-66887735	Hela-S3	cervix:	n/a	chr11:66887263-66887273
34	MAX	chr11:66886284-66886730	MCF-7	breast:	n/a	n/a
35	CTCF	chr11:66886448-66886623	GM10266	blood:	n/a	n/a
36	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
37	JUND	chr11:66886342-66886867	K562	blood:	n/a	n/a
38	EGR1	chr11:66886140-66886950	MCF-7	breast:	n/a	chr11:66886553-66886562 chr11:66886655-66886668 chr11:66886275-66886288 chr11:66886552-66886561 chr11:66886595-66886604 chr11:66886596-66886605 chr11:66886439-66886453 chr11:66886654-66886669 chr11:66886699-66886708 chr11:66886387-66886396 chr11:66886355-66886365
39	EP300	chr11:66886366-66886778	T-47D	breast:	n/a	n/a
40	REST	chr11:66886544-66887097	HL-60	blood:	n/a	chr11:66886843-66886851 chr11:66886613-66886626
41	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
42	POLR2A	chr11:66886609-66886984	IMR90	lung:	n/a	n/a
43	MAX	chr11:66886235-66886781	NB4	blood:	n/a	n/a
44	TAF1	chr11:66886465-66886967	Hela-S3	cervix:	n/a	n/a
45	HDAC2	chr11:66886463-66886651	H1-hESC	embryonic stem cell:	n/a	chr11:66886551-66886560 chr11:66886596-66886605 chr11:66886553-66886562
46	NRF1	chr11:66886187-66886898	GM12878	blood:	n/a	chr11:66886386-66886395 chr11:66886553-66886562 chr11:66886386-66886397 chr11:66886383-66886397 chr11:66886386-66886400 chr11:66886551-66886565 chr11:66886700-66886709 chr11:66886548-66886562 chr11:66886596-66886605 chr11:66886594-66886605 chr11:66886698-66886709 chr11:66886698-66886709 chr11:66886698-66886712 chr11:66886360-66886369 chr11:66886551-66886562
47	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
48	CTCF	chr11:66886382-66886640	NHEK	skin:	n/a	n/a
49	MAZ	chr11:66885004-66887904	IMR90	lung:	n/a	chr11:66886120-66886129 chr11:66886002-66886011 chr11:66887263-66887273
50	EGR1	chr11:66886272-66886631	H1-hESC	embryonic stem cell:	n/a	chr11:66886553-66886562 chr11:66886275-66886288 chr11:66886552-66886561 chr11:66886595-66886604 chr11:66886596-66886605 chr11:66886439-66886453 chr11:66886387-66886396 chr11:66886355-66886365

No.	Distal block	Cell Line	Cell type
1	chr11:66885940..66887950-chr11:67395860..67397869,2	K562	blood:
2	chr11:66885437..66888305-chr11:67055921..67058495,2	MCF-7	breast:
3	chr11:66821625..66825972-chr11:66885437..66888104,7	MCF-7	breast:
4	chr11:66885158..66886682-chr11:67030764..67032501,2	K562	blood:
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	chr11:66821404..66826403-chr11:66884710..66889541,16	MCF-7	breast:
9	chr11:66883623..66889678-chr11:67005085..67009894,16	K562	blood:

Variant related genes	Relation type
KDM2A	TF binding region
ENSG00000173120	Chromatin interaction
ENSG00000173156	Chromatin interaction
ENSG00000172932	Chromatin interaction
ENSG00000072210	Chromatin interaction
ENSG00000167799	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	chr11:66881000-66886800	Weak transcription	K562	blood
2	chr11:66884800-66888800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr11:66884800-66889200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr11:66885000-66886800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr11:66885000-66887200	Weak transcription	Fetal Brain Male	brain
6	chr11:66885000-66888600	Active TSS	Brain Substantia Nigra	brain
7	chr11:66885000-66888800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:66885000-66888800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:66885000-66889000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:66885000-66889000	Active TSS	Lung	lung
11	chr11:66885000-66889000	Active TSS	Osteobl	bone
12	chr11:66885000-66889200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr11:66885000-66889600	Active TSS	Psoas Muscle	Psoas
14	chr11:66885000-66889800	Active TSS	Fetal Brain Female	brain
15	chr11:66885000-66889800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr11:66885200-66886800	Weak transcription	Fetal Kidney	kidney
17	chr11:66885200-66887400	Weak transcription	Fetal Heart	heart
18	chr11:66885200-66887600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr11:66885200-66887800	Active TSS	Spleen	Spleen
20	chr11:66885200-66888000	Active TSS	Primary T cells from cord blood	blood
21	chr11:66885200-66888400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:66885200-66888400	Active TSS	Brain Cingulate Gyrus	brain
23	chr11:66885200-66888400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr11:66885200-66888600	Active TSS	Duodenum Mucosa	Duodenum
25	chr11:66885200-66888600	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr11:66885200-66888800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr11:66885200-66888800	Active TSS	Esophagus	oesophagus
28	chr11:66885200-66888800	Active TSS	Gastric	stomach
29	chr11:66885200-66889000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr11:66885200-66889000	Active TSS	H9 Cell Line	embryonic stem cell
31	chr11:66885200-66889000	Active TSS	Brain Angular Gyrus	brain
32	chr11:66885200-66889000	Active TSS	Colon Smooth Muscle	Colon
33	chr11:66885200-66889000	Active TSS	Placenta Amnion	Placenta Amnion
34	chr11:66885200-66889200	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr11:66885200-66889200	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr11:66885200-66889200	Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr11:66885200-66889400	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr11:66885200-66889400	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr11:66885200-66889400	Active TSS	Brain Hippocampus Middle	brain
40	chr11:66885200-66889600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:66885200-66889600	Active TSS	Ovary	ovary
42	chr11:66885200-66889800	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr11:66885200-66889800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:66885200-66890000	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr11:66885200-66890000	Active TSS	HSMM	muscle
46	chr11:66885200-66890400	Active TSS	Brain Germinal Matrix	brain
47	chr11:66885200-66890600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr11:66885400-66886800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr11:66885400-66886800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr11:66885400-66886800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links