Variant report

Variant	rs62162470
Chromosome Location	chr2:112703041-112703042
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	FOXA2	chr2:112701929-112703054	HepG2	liver:	n/a	n/a
2	JUND	chr2:112702998-112703344	HepG2	liver:	n/a	chr2:112703168-112703177
3	TEAD4	chr2:112702204-112703083	HepG2	liver:	n/a	n/a
4	CHD2	chr2:112702935-112704200	HepG2	liver:	n/a	n/a
5	ARID3A	chr2:112702097-112703171	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:112702193..112704851-chr2:112709463..112711214,2	MCF-7	breast:
2	chr2:112702698..112705516-chr2:112708749..112712467,4	K562	blood:
3	chr2:112702753..112705481-chr2:112717991..112720713,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225496	TF binding region
ENSG00000232277	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs62157784	1.00[AFR][1000 genomes]
rs62161117	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62162472	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728297	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1801950	chr2:111899783-112746937	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	esv2757825	chr2:111899783-112746937	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	esv2759083	chr2:111899783-112746937	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
7	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv998028	chr2:112649472-112734015	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv582701	chr2:112649472-112740597	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv526647	chr2:112651316-112738562	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv582702	chr2:112651316-112738562	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv1002027	chr2:112679182-112861534	Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
16	nsv999746	chr2:112691270-112796083	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	nsv1003129	chr2:112691270-112816694	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
18	esv2760607	chr2:112691282-112803423	Weak transcription Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	nsv431491	chr2:112699350-112793981	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv515698	chr2:112699350-112795908	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112678000-112705600	Weak transcription	Esophagus	oesophagus
2	chr2:112682400-112703200	Weak transcription	Placenta	Placenta
3	chr2:112683200-112703200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:112684800-112705200	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:112685600-112703200	Weak transcription	Right Ventricle	heart
6	chr2:112687000-112703600	Weak transcription	Fetal Kidney	kidney
7	chr2:112688400-112703200	Weak transcription	Fetal Intestine Large	intestine
8	chr2:112688800-112703600	Weak transcription	Aorta	Aorta
9	chr2:112689000-112703200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:112689000-112703200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:112689200-112734400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:112691400-112705200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:112693000-112703200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:112693200-112712600	Weak transcription	Spleen	Spleen
15	chr2:112696800-112703200	Weak transcription	Brain Substantia Nigra	brain
16	chr2:112698200-112703600	Weak transcription	Adipose Nuclei	Adipose
17	chr2:112698600-112712800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:112699000-112705600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:112700400-112705000	Weak transcription	HUVEC	blood vessel
20	chr2:112700800-112704400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:112701200-112703800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:112702200-112704800	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr2:112702200-112705200	Enhancers	Duodenum Mucosa	Duodenum
24	chr2:112702200-112705200	Enhancers	Stomach Smooth Muscle	stomach
25	chr2:112702200-112705600	Enhancers	Brain Angular Gyrus	brain
26	chr2:112702200-112705800	Enhancers	Colon Smooth Muscle	Colon
27	chr2:112702200-112707200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:112702200-112707600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:112702400-112704000	Enhancers	Small Intestine	intestine
30	chr2:112702400-112705400	Enhancers	Stomach Mucosa	stomach
31	chr2:112702400-112707200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr2:112702600-112703200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:112702600-112703600	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr2:112702600-112705800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr2:112702800-112703200	Enhancers	Rectal Smooth Muscle	rectum
36	chr2:112702800-112703400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:112702800-112704000	Enhancers	Pancreas	Pancrea
38	chr2:112703000-112703200	Enhancers	Fetal Lung	lung
39	chr2:112703000-112703200	Transcr. at gene 5' and 3'	HepG2	liver
40	chr2:112703000-112703400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:112703000-112703400	Genic enhancers	Left Ventricle	heart
42	chr2:112703000-112703600	Strong transcription	Fetal Stomach	stomach
43	chr2:112703000-112703800	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:112703000-112703800	Genic enhancers	Fetal Intestine Small	intestine
45	chr2:112703000-112703800	Enhancers	Gastric	stomach
46	chr2:112703000-112703800	Genic enhancers	Lung	lung
47	chr2:112703000-112703800	Enhancers	Ovary	ovary
48	chr2:112703000-112704200	Genic enhancers	Liver	Liver
49	chr2:112703000-112704400	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr2:112703000-112704800	Enhancers	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links