Variant report

Variant	rs12620839
Chromosome Location	chr2:33359457-33359458
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	CTCF	chr2:33359440-33359590	HFF-Myc	foreskin:	n/a	n/a
2	CTCF	chr2:33359360-33359510	BE2_C	brain:	n/a	n/a
3	CTCF	chr2:33359360-33359510	HEEpiC	esophagus:	n/a	n/a
4	CTCF	chr2:33359380-33359530	HRPEpiC	eye:	n/a	n/a
5	REST	chr2:33359283-33359745	SK-N-SH	brain:	n/a	chr2:33359303-33359323
6	FOS	chr2:33359185-33359778	MCF10A-Er-Src	breast:	n/a	n/a
7	CTCF	chr2:33359320-33359470	HFF	foreskin:	n/a	n/a
8	TCF12	chr2:33358284-33360435	SK-N-SH	brain:	n/a	n/a
9	CTCF	chr2:33359380-33359530	HMEC	breast:	n/a	n/a
10	FOSL2	chr2:33359202-33359864	A549	lung:	n/a	n/a
11	JUND	chr2:33358970-33359932	SK-N-SH	brain:	n/a	n/a
12	EP300	chr2:33359185-33359753	SK-N-SH_RA	brain:	n/a	n/a
13	CTCF	chr2:33359340-33359490	HMF	breast:	n/a	n/a
14	REST	chr2:33359223-33359811	SK-N-SH	brain:	n/a	chr2:33359303-33359323
15	CTCF	chr2:33359380-33359530	HMF	breast:	n/a	n/a
16	JUND	chr2:33359050-33359979	SK-N-SH	brain:	n/a	n/a
17	MAFK	chr2:33359197-33359898	IMR90	lung:	n/a	n/a
18	STAT3	chr2:33359091-33359717	MCF10A-Er-Src	breast:	n/a	n/a
19	YY1	chr2:33359265-33359702	SK-N-SH_RA	brain:	n/a	n/a
20	EP300	chr2:33359036-33359963	SK-N-SH	brain:	n/a	n/a
21	NFIC	chr2:33359104-33359911	SK-N-SH	brain:	n/a	n/a
22	CTCF	chr2:33359380-33359530	SK-N-SH_RA	brain:	n/a	n/a
23	FOSL2	chr2:33358873-33359926	SK-N-SH	brain:	n/a	n/a
24	CTCF	chr2:33359400-33359550	AG09319	gingival:	n/a	n/a
25	CTCF	chr2:33359380-33359530	BE2_C	brain:	n/a	n/a
26	CTCF	chr2:33359400-33359550	AoAF	blood vessel:	n/a	n/a
27	POLR2A	chr2:33359080-33362022	SK-N-SH	brain:	n/a	n/a
28	CTCF	chr2:33359400-33359550	HEEpiC	esophagus:	n/a	n/a
29	POLR2A	chr2:33359225-33360301	U87	brain:	n/a	n/a
30	USF1	chr2:33358923-33360045	SK-N-SH	brain:	n/a	n/a
31	CTCF	chr2:33359420-33359570	SK-N-SH_RA	brain:	n/a	n/a
32	CTCF	chr2:33359380-33359530	AG10803	skin:	n/a	n/a
33	STAT3	chr2:33359133-33359710	MCF10A-Er-Src	breast:	n/a	n/a
34	CTCF	chr2:33359380-33359530	AG04449	skin:	n/a	n/a
35	CTCF	chr2:33359340-33359490	HVMF	connective:	n/a	n/a
36	POLR2A	chr2:33359034-33363189	MCF10A-Er-Src	breast:	n/a	n/a
37	E2F4	chr2:33359242-33359864	MCF10A-Er-Src	breast:	n/a	n/a
38	CTCF	chr2:33359377-33359564	Gliobla	brain:	n/a	n/a
39	CTCF	chr2:33359380-33359530	NHDF-neo	bronchial:	n/a	n/a
40	CTCF	chr2:33359420-33359570	A549	lung:	n/a	n/a
41	POLR2A	chr2:33358958-33362720	MCF10A-Er-Src	breast:	n/a	n/a
42	CTCF	chr2:33359380-33359530	AoAF	blood vessel:	n/a	n/a
43	KAP1	chr2:33359319-33359702	U2OS	brain:	n/a	chr2:33359663-33359671
44	CTCF	chr2:33359320-33359470	NHEK	skin:	n/a	n/a
45	CTCF	chr2:33359380-33359530	BJ	skin:	n/a	n/a
46	FOXA2	chr2:33359302-33359913	A549	lung:	n/a	n/a
47	MAX	chr2:33359114-33359909	SK-N-SH	brain:	n/a	n/a
48	MYC	chr2:33359170-33360493	MCF10A-Er-Src	breast:	n/a	chr2:33360266-33360277
49	CTCF	chr2:33359360-33359510	HUVEC	blood vessel:	n/a	n/a
50	FOS	chr2:33359068-33360093	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
LTBP1	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1545550	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17012569	0.82[MEX][hapmap]
rs4670256	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4952342	0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	esv33628	chr2:33257484-33455355	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1012946	chr2:33294522-33370391	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv535626	chr2:33294522-33370391	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv873789	chr2:33297967-33390188	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33358200-33359800	Enhancers	Monocytes-CD14+_RO01746	blood
2	chr2:33358400-33359600	Enhancers	HUVEC	blood vessel
3	chr2:33358400-33359600	Flanking Active TSS	Osteobl	bone
4	chr2:33358400-33360000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr2:33358400-33360000	Enhancers	K562	blood
6	chr2:33358400-33360600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:33358400-33361200	Active TSS	Brain Cingulate Gyrus	brain
8	chr2:33358600-33360200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:33358600-33360200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:33358600-33360200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:33358600-33360200	Flanking Active TSS	Fetal Heart	heart
12	chr2:33358600-33360400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:33358600-33361200	Active TSS	Brain Anterior Caudate	brain
14	chr2:33358600-33362000	Active TSS	Brain Angular Gyrus	brain
15	chr2:33358600-33362600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr2:33358800-33359600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:33358800-33359600	Enhancers	Esophagus	oesophagus
18	chr2:33358800-33359600	Enhancers	NHEK	skin
19	chr2:33358800-33359800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:33358800-33359800	Weak transcription	Placenta	Placenta
21	chr2:33358800-33359800	Weak transcription	Lung	lung
22	chr2:33358800-33360000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:33358800-33360000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr2:33358800-33360000	Flanking Active TSS	Liver	Liver
25	chr2:33358800-33360000	Active TSS	Brain Hippocampus Middle	brain
26	chr2:33358800-33360000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr2:33358800-33361200	Weak transcription	Gastric	stomach
28	chr2:33358800-33362000	Active TSS	Ovary	ovary
29	chr2:33358800-33363200	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr2:33358800-33371600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:33359000-33360200	Flanking Active TSS	HSMM	muscle
32	chr2:33359000-33362000	Active TSS	Psoas Muscle	Psoas
33	chr2:33359000-33362000	Active TSS	Right Atrium	heart
34	chr2:33359000-33362800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:33359000-33362800	Active TSS	Aorta	Aorta
36	chr2:33359000-33363000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:33359000-33363000	Active TSS	Stomach Smooth Muscle	stomach
38	chr2:33359200-33359600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:33359200-33359600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:33359200-33360000	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr2:33359200-33360200	Flanking Active TSS	A549	lung
42	chr2:33359200-33360200	Bivalent Enhancer	HepG2	liver
43	chr2:33359200-33360400	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr2:33359200-33360600	Active TSS	Fetal Lung	lung
45	chr2:33359200-33361200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:33359200-33361200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:33359200-33361200	Active TSS	Brain Substantia Nigra	brain
48	chr2:33359200-33361600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:33359200-33362000	Active TSS	Right Ventricle	heart
50	chr2:33359200-33362600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links