Variant report

Variant	rs9862206
Chromosome Location	chr3:53194319-53194320
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	chr3:53194240-53194390	NHLF	lung:	n/a	n/a
2	ZKSCAN1	chr3:53194146-53195105	Hela-S3	cervix:	n/a	n/a
3	HNF4G	chr3:53194014-53194407	HepG2	liver:	n/a	chr3:53194212-53194227 chr3:53194212-53194227 chr3:53194210-53194228 chr3:53194213-53194225 chr3:53194213-53194225 chr3:53194212-53194227 chr3:53194218-53194226 chr3:53194212-53194226 chr3:53194210-53194225 chr3:53194212-53194227 chr3:53194212-53194226 chr3:53194213-53194226
4	CEBPB	chr3:53194012-53194326	HepG2	liver:	n/a	chr3:53194181-53194194
5	RCOR1	chr3:53194157-53195879	IMR90	lung:	n/a	n/a
6	CTCF	chr3:53194200-53194350	GM12865	blood:	n/a	n/a
7	CTCF	chr3:53194200-53194350	HPAF	blood vessel:	n/a	n/a
8	HNF4A	chr3:53194085-53194322	HepG2	liver:	n/a	chr3:53194212-53194227 chr3:53194212-53194227 chr3:53194210-53194228 chr3:53194213-53194225 chr3:53194213-53194225 chr3:53194212-53194227 chr3:53194218-53194226 chr3:53194211-53194226 chr3:53194212-53194226 chr3:53194212-53194227 chr3:53194212-53194226 chr3:53194213-53194226
9	MXI1	chr3:53193378-53195621	HepG2	liver:	n/a	n/a
10	HNF4A	chr3:53194062-53194373	HepG2	liver:	n/a	chr3:53194212-53194227 chr3:53194212-53194227 chr3:53194210-53194228 chr3:53194213-53194225 chr3:53194213-53194225 chr3:53194212-53194227 chr3:53194218-53194226 chr3:53194211-53194226 chr3:53194212-53194226 chr3:53194212-53194227 chr3:53194212-53194226 chr3:53194213-53194226
11	HNF4G	chr3:53193347-53194323	HepG2	liver:	n/a	chr3:53193694-53193707 chr3:53193693-53193707 chr3:53193693-53193706 chr3:53194212-53194227 chr3:53193694-53193706 chr3:53193694-53193706 chr3:53193694-53193706 chr3:53194212-53194227 chr3:53194210-53194228 chr3:53193689-53193711 chr3:53193691-53193709 chr3:53194213-53194225 chr3:53194213-53194225 chr3:53194212-53194227 chr3:53194218-53194226 chr3:53193693-53193707 chr3:53193691-53193706 chr3:53193694-53193706 chr3:53194212-53194226 chr3:53194210-53194225 chr3:53193698-53193710 chr3:53194212-53194227 chr3:53193693-53193706 chr3:53194212-53194226 chr3:53194213-53194226 chr3:53193693-53193706 chr3:53193695-53193707
12	MTA3	chr3:53194172-53195140	GM12878	blood:	n/a	n/a
13	STAT5A	chr3:53194177-53195189	GM12878	blood:	n/a	chr3:53195045-53195057 chr3:53194688-53194696
14	CTCF	chr3:53194310-53195119	A549	lung:	n/a	chr3:53194938-53194951
15	POLR2A	chr3:53193966-53197708	GM12891	blood:	n/a	n/a
16	HNF4A	chr3:53193100-53194325	HepG2	liver:	n/a	chr3:53193694-53193707 chr3:53193693-53193707 chr3:53193693-53193706 chr3:53194212-53194227 chr3:53193694-53193706 chr3:53193694-53193706 chr3:53193694-53193706 chr3:53194212-53194227 chr3:53194210-53194228 chr3:53193689-53193711 chr3:53193691-53193709 chr3:53194213-53194225 chr3:53194213-53194225 chr3:53194212-53194227 chr3:53194218-53194226 chr3:53193693-53193707 chr3:53194211-53194226 chr3:53193694-53193706 chr3:53194212-53194226 chr3:53193698-53193710 chr3:53194212-53194227 chr3:53193692-53193707 chr3:53193693-53193706 chr3:53194212-53194226 chr3:53194213-53194226 chr3:53193693-53193706 chr3:53193695-53193707
17	POLR2A	chr3:53193238-53194614	HepG2	liver:	n/a	n/a
18	PML	chr3:53194258-53195292	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:53172874..53174968-chr3:53193590..53195106,2	MCF-7	breast:
2	chr3:53194109..53196337-chr3:53288407..53290127,2	MCF-7	breast:
3	chr3:53160337..53170540-chr3:53189028..53198029,25	MCF-7	breast:
4	chr3:53150117..53153813-chr3:53191442..53194922,3	MCF-7	breast:
5	chr3:53167017..53169952-chr3:53191720..53194469,2	K562	blood:

Variant related genes	Relation type
PRKCD	TF binding region
ENSG00000163933	Chromatin interaction
ENSG00000163931	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs13319192	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035451	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56972966	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59254509	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72967449	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750527	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750528	0.86[EUR][1000 genomes];1.00[ASN][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
rs9862206	TKT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53183200-53194600	Enhancers	Gastric	stomach
2	chr3:53183400-53194600	Enhancers	Pancreas	Pancrea
3	chr3:53184200-53194400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:53187800-53194600	Enhancers	Esophagus	oesophagus
5	chr3:53190600-53194400	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr3:53190800-53194600	Enhancers	Lung	lung
7	chr3:53191000-53194400	Enhancers	Fetal Intestine Small	intestine
8	chr3:53191200-53194400	Enhancers	Placenta	Placenta
9	chr3:53191400-53194400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr3:53191400-53194400	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:53191400-53194400	Enhancers	Fetal Intestine Large	intestine
12	chr3:53191800-53194400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr3:53191800-53194400	Enhancers	Right Ventricle	heart
14	chr3:53192000-53194600	Enhancers	Primary B cells from peripheral blood	blood
15	chr3:53192200-53194400	Enhancers	Primary B cells from cord blood	blood
16	chr3:53192400-53194600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:53192400-53194600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:53192400-53194600	Enhancers	Liver	Liver
19	chr3:53192600-53194400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:53192600-53194600	Enhancers	Fetal Kidney	kidney
21	chr3:53192600-53194600	Flanking Active TSS	HepG2	liver
22	chr3:53192600-53194800	Enhancers	Spleen	Spleen
23	chr3:53192800-53194400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
24	chr3:53192800-53194400	Enhancers	Right Atrium	heart
25	chr3:53192800-53194400	Enhancers	HUVEC	blood vessel
26	chr3:53192800-53194600	Enhancers	Fetal Lung	lung
27	chr3:53193000-53194400	Weak transcription	Aorta	Aorta
28	chr3:53193200-53194400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
29	chr3:53193200-53194400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:53193200-53194400	Enhancers	Left Ventricle	heart
31	chr3:53193200-53194600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:53193200-53194600	Enhancers	Ovary	ovary
33	chr3:53193400-53194400	Enhancers	H9 Cell Line	embryonic stem cell
34	chr3:53193400-53194400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
35	chr3:53193400-53194400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:53193400-53194400	Enhancers	Brain Substantia Nigra	brain
37	chr3:53193400-53194400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr3:53193400-53194400	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr3:53193400-53194400	Enhancers	Psoas Muscle	Psoas
40	chr3:53193400-53194600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:53193400-53194600	Bivalent Enhancer	Fetal Stomach	stomach
42	chr3:53193400-53194800	Flanking Active TSS	Hela-S3	cervix
43	chr3:53193600-53194400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:53193600-53194400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:53193600-53195200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr3:53193800-53194400	Enhancers	Primary hematopoietic stem cells	blood
47	chr3:53193800-53194400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr3:53193800-53194600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
49	chr3:53193800-53194600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr3:53193800-53194800	Flanking Active TSS	Adipose Nuclei	Adipose

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