Variant report

Variant	rs12622056
Chromosome Location	chr2:233753167-233753168
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:233752931-233753248	GM19239	blood:	n/a	n/a
2	POLR2A	chr2:233752848-233753204	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr2:233751474-233753914	HepG2	liver:	n/a	n/a
4	CHD2	chr2:233753157-233753237	HepG2	liver:	n/a	n/a
5	MAX	chr2:233752995-233753239	H1-hESC	embryonic stem cell:	n/a	n/a
6	SUZ12	chr2:233752920-233753265	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr2:233752937-233753221	Gliobla	brain:	n/a	n/a
8	CTCF	chr2:233753116-233753180	NHEK	skin:	n/a	n/a
9	POLR2A	chr2:233753002-233753227	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:233752633-233753414	HepG2	liver:	n/a	n/a
11	BHLHE40	chr2:233753008-233753198	K562	blood:	n/a	n/a
12	POLR2A	chr2:233752875-233753262	HepG2	liver:	n/a	n/a
13	NFATC1	chr2:233752878-233753179	GM12878	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:233746909..233748527-chr2:233752427..233754026,2	MCF-7	breast:
2	chr2:233746656..233750390-chr2:233751961..233755416,5	K562	blood:
3	chr2:233748622..233750691-chr2:233751961..233754104,3	K562	blood:

No data

Variant related genes	Relation type
NGEF	TF binding region
ENSG00000066248	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12612786	0.81[EUR][1000 genomes]
rs2241979	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3738902	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72617183	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72617184	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1009825	chr2:233709566-233763470	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv984452	chr2:233725452-233762965	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv999116	chr2:233733352-233759864	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1007029	chr2:233733352-233760519	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv536179	chr2:233735380-233757170	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv3375822	chr2:233750908-233755306	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233726800-233755600	Weak transcription	HSMMtube	muscle
2	chr2:233742400-233754200	Strong transcription	Fetal Intestine Small	intestine
3	chr2:233742400-233755600	Weak transcription	Fetal Intestine Large	intestine
4	chr2:233742600-233753400	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr2:233742800-233755600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:233743000-233755800	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:233743200-233759600	Strong transcription	Duodenum Mucosa	Duodenum
8	chr2:233744600-233755400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:233745200-233755600	Weak transcription	Brain Angular Gyrus	brain
10	chr2:233745200-233755800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:233745600-233759800	Strong transcription	Liver	Liver
12	chr2:233746000-233753200	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr2:233749200-233755600	Weak transcription	NHLF	lung
14	chr2:233749400-233766000	Weak transcription	A549	lung
15	chr2:233749800-233753400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:233750000-233755600	Weak transcription	Brain Germinal Matrix	brain
17	chr2:233750600-233755400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:233750600-233759800	Strong transcription	HepG2	liver
19	chr2:233750800-233761000	Weak transcription	Stomach Mucosa	stomach
20	chr2:233751000-233755600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:233751000-233766000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:233751200-233753400	Strong transcription	Esophagus	oesophagus
23	chr2:233751200-233755400	Weak transcription	Pancreas	Pancrea
24	chr2:233751200-233755600	Weak transcription	Fetal Brain Female	brain
25	chr2:233751200-233755600	Weak transcription	Gastric	stomach
26	chr2:233751200-233758400	Weak transcription	Fetal Brain Male	brain
27	chr2:233751800-233755800	Weak transcription	Right Atrium	heart
28	chr2:233752400-233753200	Strong transcription	Colonic Mucosa	Colon
29	chr2:233752400-233754400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:233752600-233753200	Enhancers	H1 Cell Line	embryonic stem cell
31	chr2:233752800-233753200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:233752800-233753200	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr2:233752800-233753400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:233752800-233753400	Enhancers	Spleen	Spleen
35	chr2:233753000-233753200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:233753000-233753200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
37	chr2:233753000-233753200	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr2:233753000-233753200	ZNF genes & repeats	Fetal Kidney	kidney
39	chr2:233753000-233753200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:233753000-233753400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:233753000-233753400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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