Variant report

Variant	rs56352405
Chromosome Location	chr2:11883818-11883819
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	RCOR1	chr2:11883701-11885172	IMR90	lung:	n/a	n/a
2	RCOR1	chr2:11883662-11884721	K562	blood:	n/a	n/a
3	FOSL1	chr2:11883773-11885150	HCT-116	colon:	n/a	chr2:11884384-11884396 chr2:11884385-11884395 chr2:11884385-11884395 chr2:11884386-11884394 chr2:11884299-11884310 chr2:11883863-11883874 chr2:11884385-11884395
4	NR2F2	chr2:11883634-11885680	K562	blood:	n/a	n/a
5	RCOR1	chr2:11882940-11885622	K562	blood:	n/a	n/a
6	CTCF	chr2:11883295-11885691	A549	lung:	n/a	chr2:11883633-11883646 chr2:11883630-11883643 chr2:11883635-11883645
7	SP1	chr2:11883699-11885017	HCT-116	colon:	n/a	chr2:11884267-11884281
8	CBX3	chr2:11883750-11884666	K562	blood:	n/a	n/a
9	MAX	chr2:11882665-11883923	HepG2	liver:	n/a	chr2:11882967-11882977
10	ELF1	chr2:11883368-11884038	GM12878	blood:	n/a	n/a
11	TBP	chr2:11883747-11884615	K562	blood:	n/a	n/a
12	MXI1	chr2:11883755-11885707	SK-N-SH	brain:	n/a	n/a
13	NFIC	chr2:11883814-11884780	GM12878	blood:	n/a	n/a
14	PML	chr2:11883795-11884753	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:11883176-11885464	K562	blood:	n/a	n/a
16	JUND	chr2:11883498-11885610	SK-N-SH	brain:	n/a	chr2:11884384-11884396 chr2:11884385-11884395 chr2:11884385-11884395 chr2:11884386-11884394 chr2:11883863-11883874 chr2:11884384-11884395 chr2:11884385-11884395
17	SP1	chr2:11883763-11885003	HCT-116	colon:	n/a	chr2:11884267-11884281
18	TCF12	chr2:11883698-11885051	A549	lung:	n/a	n/a
19	JUN	chr2:11882263-11884893	K562	blood:	n/a	chr2:11884384-11884396 chr2:11884385-11884395 chr2:11882641-11882652 chr2:11884385-11884395 chr2:11884386-11884394 chr2:11882644-11882655 chr2:11882643-11882651 chr2:11883863-11883874 chr2:11882641-11882653 chr2:11884385-11884395
20	SIX5	chr2:11883731-11885008	A549	lung:	n/a	chr2:11884088-11884097
21	MAX	chr2:11883780-11885650	A549	lung:	n/a	n/a
22	FOSL2	chr2:11883640-11885047	A549	lung:	n/a	chr2:11884384-11884396 chr2:11884385-11884395 chr2:11884385-11884395 chr2:11884386-11884394 chr2:11883863-11883874 chr2:11884300-11884311 chr2:11884385-11884395
23	MAZ	chr2:11883792-11885194	IMR90	lung:	n/a	n/a
24	SIN3AK20	chr2:11883805-11884805	MCF-7	breast:	n/a	n/a
25	RAD21	chr2:11883135-11888795	SK-N-SH	brain:	n/a	chr2:11888754-11888767 chr2:11883562-11883572 chr2:11883630-11883644
26	SP1	chr2:11883781-11885110	A549	lung:	n/a	chr2:11884267-11884281
27	SMC3	chr2:11883257-11885766	SK-N-SH	brain:	n/a	chr2:11883632-11883646

No.	Distal block	Cell Line	Cell type
1	chr2:11883702..11885372-chr2:11901343..11903845,2	K562	blood:
2	chr2:11881178..11885762-chr2:11886043..11889477,7	MCF-7	breast:
3	chr2:11882438..11884776-chr2:11910789..11914613,4	K562	blood:
4	chr2:11882508..11884186-chr2:11887506..11889026,2	MCF-7	breast:
5	chr2:11604833..11608003-chr2:11882353..11886330,4	K562	blood:
6	chr2:11882411..11885202-chr2:11902345..11904670,2	K562	blood:

Variant related genes	Relation type
LPIN1	TF binding region
ENSG00000169016	Chromatin interaction
ENSG00000134324	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10183250	1.00[EUR][1000 genomes]
rs11884138	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11886664	1.00[EUR][1000 genomes]
rs11890221	1.00[EUR][1000 genomes]
rs11895768	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13420559	1.00[EUR][1000 genomes]
rs13421766	1.00[EUR][1000 genomes]
rs13424731	1.00[EUR][1000 genomes]
rs16857649	1.00[EUR][1000 genomes]
rs16857699	1.00[EUR][1000 genomes]
rs55736020	1.00[EUR][1000 genomes]
rs56820808	1.00[EUR][1000 genomes]
rs56834951	1.00[EUR][1000 genomes]
rs57779431	1.00[EUR][1000 genomes]
rs58686966	1.00[EUR][1000 genomes]
rs59101452	1.00[EUR][1000 genomes]
rs59157966	1.00[EUR][1000 genomes]
rs59416046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59836200	1.00[EUR][1000 genomes]
rs61382095	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6745921	1.00[EUR][1000 genomes]
rs6755991	1.00[AMR][1000 genomes]
rs73185109	1.00[EUR][1000 genomes]
rs73917104	1.00[EUR][1000 genomes]
rs73917107	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73917124	1.00[EUR][1000 genomes]
rs73917127	1.00[EUR][1000 genomes]
rs7562399	1.00[EUR][1000 genomes]
rs7585718	1.00[EUR][1000 genomes]
rs7602962	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv580973	chr2:11864946-11898931	Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv580974	chr2:11867841-11898931	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11879200-11884000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr2:11879200-11884400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr2:11879400-11884000	Weak transcription	Adipose Nuclei	Adipose
4	chr2:11879600-11884000	Weak transcription	Osteobl	bone
5	chr2:11879800-11884400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:11881600-11884800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:11882000-11884200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:11882000-11884400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr2:11882200-11884200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:11882200-11884200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:11882200-11884400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:11882200-11884400	Enhancers	Hela-S3	cervix
13	chr2:11882200-11884400	Enhancers	HMEC	breast
14	chr2:11882200-11884400	Enhancers	NHLF	lung
15	chr2:11882400-11884000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:11882400-11884400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr2:11882400-11884400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:11882400-11884400	Enhancers	HUVEC	blood vessel
19	chr2:11882400-11886200	Enhancers	NHDF-Ad	bronchial
20	chr2:11882600-11885400	Flanking Bivalent TSS/Enh	HepG2	liver
21	chr2:11882600-11886800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:11882800-11885200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr2:11882800-11885400	Enhancers	Pancreas	Pancrea
24	chr2:11882800-11886000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:11882800-11886200	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:11882800-11886400	Enhancers	Fetal Thymus	thymus
27	chr2:11882800-11886600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:11883000-11884000	Enhancers	Gastric	stomach
29	chr2:11883000-11885200	Enhancers	H1 Cell Line	embryonic stem cell
30	chr2:11883000-11885200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:11883000-11885200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:11883000-11885600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:11883000-11886200	Enhancers	Fetal Muscle Leg	muscle
34	chr2:11883200-11884000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:11883200-11884000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:11883200-11884000	Enhancers	Fetal Kidney	kidney
37	chr2:11883200-11884000	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr2:11883200-11884400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:11883200-11884400	Flanking Active TSS	Liver	Liver
40	chr2:11883200-11884400	Enhancers	Fetal Muscle Trunk	muscle
41	chr2:11883200-11885000	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr2:11883200-11885400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:11883200-11886000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:11883400-11884000	Enhancers	Brain Cingulate Gyrus	brain
45	chr2:11883400-11884000	Enhancers	Esophagus	oesophagus
46	chr2:11883400-11884200	Enhancers	Brain Hippocampus Middle	brain
47	chr2:11883400-11884200	Enhancers	Right Atrium	heart
48	chr2:11883400-11885600	Flanking Active TSS	K562	blood
49	chr2:11883400-11886200	Enhancers	Fetal Intestine Large	intestine
50	chr2:11883400-11886200	Enhancers	Fetal Intestine Small	intestine

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