Variant report

Variant	rs7974725
Chromosome Location	chr12:104684288-104684289
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	POLR2A	chr12:104684246-104684433	HCT-116	colon:	n/a	n/a
2	POLR2A	chr12:104684159-104684289	A549	lung:	n/a	n/a
3	POLR2A	chr12:104684190-104684456	A549	lung:	n/a	n/a
4	POLR2A	chr12:104679566-104684466	PANC-1	pancreas:	n/a	n/a
5	CEBPB	chr12:104684248-104684584	A549	lung:	n/a	chr12:104684427-104684438
6	POLR2A	chr12:104680676-104684470	A549	lung:	n/a	n/a
7	CEBPB	chr12:104684263-104684559	HepG2	liver:	n/a	chr12:104684427-104684438
8	SIN3AK20	chr12:104681904-104684468	A549	lung:	n/a	n/a
9	TCF7L2	chr12:104684162-104684357	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr12:104684139-104684334	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:104684058-104684510	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr12:104684168-104684467	Hela-S3	cervix:	n/a	n/a
13	REST	chr12:104679408-104684472	A549	lung:	n/a	chr12:104680747-104680760
14	CEBPB	chr12:104684272-104684554	IMR90	lung:	n/a	chr12:104684427-104684438
15	POLR2A	chr12:104684221-104684477	A549	lung:	n/a	n/a
16	CHD1	chr12:104679486-104684470	IMR90	lung:	n/a	n/a
17	CEBPB	chr12:104684237-104684655	A549	lung:	n/a	chr12:104684427-104684438
18	POLR2A	chr12:104684129-104684456	A549	lung:	n/a	n/a
19	GATA3	chr12:104679262-104685085	A549	lung:	n/a	chr12:104683188-104683204 chr12:104683192-104683201 chr12:104683191-104683199 chr12:104683216-104683229 chr12:104683841-104683851 chr12:104683193-104683210
20	CEBPB	chr12:104684254-104684597	Hela-S3	cervix:	n/a	chr12:104684427-104684438
21	SP1	chr12:104679414-104684520	A549	lung:	n/a	chr12:104682628-104682639 chr12:104683086-104683100
22	TCF12	chr12:104679345-104685076	A549	lung:	n/a	chr12:104683753-104683760
23	POLR2A	chr12:104684043-104684459	Hela-S3	cervix:	n/a	n/a
24	JUND	chr12:104684068-104684503	A549	lung:	n/a	n/a
25	BCL3	chr12:104679505-104684468	A549	lung:	n/a	chr12:104680954-104680967 chr12:104680954-104680967
26	CEBPB	chr12:104684072-104684898	A549	lung:	n/a	chr12:104684427-104684438
27	SIX5	chr12:104679450-104684397	A549	lung:	n/a	chr12:104681208-104681217

No.	Distal block	Cell Line	Cell type
1	chr12:104606650..104616346-chr12:104679108..104687347,18	K562	blood:
2	chr12:104530429..104534144-chr12:104679811..104684673,6	MCF-7	breast:
3	chr12:104611527..104621556-chr12:104677756..104684608,20	MCF-7	breast:

Variant related genes	Relation type
TXNRD1	TF binding region
ENSG00000120837	Chromatin interaction
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10861188	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861201	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861203	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111999	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112003	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1128446	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33937214	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35483264	0.87[ASN][1000 genomes]
rs4523760	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134193	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315475	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7962942	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers 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 lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104680600-104684400	Active TSS	Esophagus	oesophagus
2	chr12:104680600-104684600	Active TSS	Hela-S3	cervix
3	chr12:104682000-104687400	Transcr. at gene 5' and 3'	A549	lung
4	chr12:104682200-104684400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
5	chr12:104682400-104684400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:104682600-104685000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:104682800-104684400	Transcr. at gene 5' and 3'	Osteobl	bone
8	chr12:104682800-104685000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:104683000-104685600	Weak transcription	Small Intestine	intestine
10	chr12:104683000-104686000	Transcr. at gene 5' and 3'	HUVEC	blood vessel
11	chr12:104683200-104684400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:104683200-104687400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:104683400-104684400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:104683400-104684400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:104683400-104684400	Enhancers	Pancreas	Pancrea
16	chr12:104683400-104684400	Enhancers	Stomach Mucosa	stomach
17	chr12:104683400-104684400	Transcr. at gene 5' and 3'	HMEC	breast
18	chr12:104683400-104686600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr12:104683400-104687800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
20	chr12:104683400-104688600	Weak transcription	Brain Substantia Nigra	brain
21	chr12:104683400-104696800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:104683600-104684400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr12:104683600-104684400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:104683600-104684400	Enhancers	Placenta	Placenta
25	chr12:104683600-104684400	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr12:104683600-104684400	Transcr. at gene 5' and 3'	Dnd41	blood
27	chr12:104683600-104684600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:104683600-104684800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:104683600-104689000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr12:104683600-104690200	Weak transcription	Fetal Kidney	kidney
31	chr12:104683800-104684400	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr12:104683800-104684400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr12:104683800-104684400	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr12:104683800-104684400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr12:104683800-104684400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr12:104683800-104684400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:104683800-104684400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr12:104683800-104684400	Enhancers	Gastric	stomach
39	chr12:104683800-104684400	Active TSS	Left Ventricle	heart
40	chr12:104683800-104684400	Genic enhancers	Lung	lung
41	chr12:104683800-104684400	Enhancers	Rectal Smooth Muscle	rectum
42	chr12:104683800-104684400	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr12:104683800-104684600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:104683800-104684800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:104683800-104684800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:104683800-104684800	Weak transcription	Liver	Liver
47	chr12:104683800-104684800	Active TSS	NHLF	lung
48	chr12:104683800-104685000	Active TSS	Right Ventricle	heart
49	chr12:104683800-104685400	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr12:104683800-104685400	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links