Variant report

Variant	rs12635973
Chromosome Location	chr3:53277675-53277676
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:53277379-53278219	A549	lung:	n/a	n/a
2	FOSL2	chr3:53276915-53277782	A549	lung:	n/a	chr3:53277494-53277503
3	E2F6	chr3:53277164-53277681	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr3:53275974-53278821	A549	lung:	n/a	n/a
5	POLR2A	chr3:53277667-53278121	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:53277655-53277790	A549	lung:	n/a	n/a
7	POLR2A	chr3:53277463-53278524	Hela-S3	cervix:	n/a	n/a
8	MYC	chr3:53277228-53277943	A549	lung:	n/a	n/a
9	KAP1	chr3:53277182-53277719	U2OS	brain:	n/a	n/a
10	E2F6	chr3:53277137-53277703	H1-hESC	embryonic stem cell:	n/a	n/a
11	SP1	chr3:53277124-53278162	A549	lung:	n/a	chr3:53277456-53277468
12	MYC	chr3:53277657-53277734	HUVEC	blood vessel:	n/a	n/a
13	KAP1	chr3:53277063-53277736	HEK293	kidney:	n/a	n/a
14	E2F6	chr3:53277207-53277687	A549	lung:	n/a	n/a
15	POLR2A	chr3:53277644-53278126	A549	lung:	n/a	n/a
16	POLR2A	chr3:53277200-53278246	A549	lung:	n/a	n/a
17	POLR2A	chr3:53273486-53278931	HL-60	blood:	n/a	n/a
18	TCF12	chr3:53275798-53279013	A549	lung:	n/a	chr3:53278266-53278273 chr3:53277949-53277959 chr3:53276621-53276631
19	REST	chr3:53277539-53277723	A549	lung:	n/a	n/a
20	MAX	chr3:53276675-53278302	A549	lung:	n/a	n/a
21	E2F6	chr3:53277090-53277815	A549	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:53266350..53272175-chr3:53273806..53279972,8	K562	blood:
2	chr3:53276909..53279074-chr3:53282847..53285321,2	MCF-7	breast:
3	chr3:53272054..53273802-chr3:53276438..53278455,2	MCF-7	breast:
4	chr3:53268931..53277907-chr3:53285563..53291617,11	MCF-7	breast:
5	chr3:53268759..53271558-chr3:53275387..53277889,3	MCF-7	breast:
6	chr3:53276936..53279877-chr3:53288649..53290912,2	MCF-7	breast:
7	chr3:53267066..53270422-chr3:53274180..53278623,4	K562	blood:

No data

Variant related genes	Relation type
TKT	TF binding region
ENSG00000163931	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12629138	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs12632671	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12633047	0.90[AMR][1000 genomes]
rs41332244	1.00[CEU][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12635973	TKT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53257000-53277800	Strong transcription	Primary T helper cells fromperipheralblood	blood
2	chr3:53257400-53278800	Strong transcription	Primary T cells from cord blood	blood
3	chr3:53257400-53280200	Strong transcription	Dnd41	blood
4	chr3:53266800-53279000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:53269600-53280400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:53270000-53280000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:53270800-53278000	Strong transcription	Fetal Thymus	thymus
8	chr3:53272000-53278800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:53272000-53278800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:53272200-53278800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:53272400-53282200	Genic enhancers	Primary monocytes fromperipheralblood	blood
12	chr3:53272600-53280600	Transcr. at gene 5' and 3'	A549	lung
13	chr3:53272800-53279000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:53272800-53279600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:53272800-53286600	Weak transcription	Fetal Brain Male	brain
16	chr3:53272800-53288000	Weak transcription	Fetal Kidney	kidney
17	chr3:53273000-53278400	Genic enhancers	Hela-S3	cervix
18	chr3:53273600-53279000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr3:53274200-53278000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:53274200-53278800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:53274200-53279000	Genic enhancers	Spleen	Spleen
22	chr3:53274400-53283600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:53274600-53279000	Enhancers	Fetal Heart	heart
24	chr3:53275000-53278400	Genic enhancers	Right Ventricle	heart
25	chr3:53275000-53281600	Weak transcription	K562	blood
26	chr3:53275200-53278800	Enhancers	Right Atrium	heart
27	chr3:53275200-53279000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:53275400-53278600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr3:53275400-53283200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:53275800-53278200	Enhancers	Psoas Muscle	Psoas
31	chr3:53275800-53278800	Genic enhancers	Brain Cingulate Gyrus	brain
32	chr3:53275800-53279000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
33	chr3:53276000-53278000	Genic enhancers	HMEC	breast
34	chr3:53276000-53278400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:53276000-53278600	Genic enhancers	NHDF-Ad	bronchial
36	chr3:53276000-53278800	Genic enhancers	Esophagus	oesophagus
37	chr3:53276000-53278800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr3:53276000-53283400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:53276200-53277800	Weak transcription	Aorta	Aorta
40	chr3:53276200-53278400	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr3:53276200-53278600	Genic enhancers	Fetal Intestine Small	intestine
42	chr3:53276200-53278800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr3:53276200-53279000	Enhancers	Placenta	Placenta
44	chr3:53276200-53279400	Weak transcription	Brain Germinal Matrix	brain
45	chr3:53276200-53279600	Enhancers	Pancreas	Pancrea
46	chr3:53276200-53283800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:53276200-53287400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:53276400-53277800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:53276400-53277800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:53276400-53278600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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