Variant report

Variant	rs57554435
Chromosome Location	chr17:38179803-38179804
allele	A/G
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	chr17:38179649-38180461	HUVEC	blood vessel:	n/a	n/a
2	TFAP2A	chr17:38179544-38180216	Hela-S3	cervix:	n/a	chr17:38179948-38179959 chr17:38180001-38180016 chr17:38179947-38179959
3	POLR2A	chr17:38179546-38179886	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr17:38179255-38179905	K562	blood:	n/a	n/a
5	MYC	chr17:38179544-38180256	MCF10A-Er-Src	breast:	n/a	n/a
6	MAX	chr17:38179366-38179888	MCF-7	breast:	n/a	n/a
7	STAT3	chr17:38179539-38180379	MCF10A-Er-Src	breast:	n/a	chr17:38180099-38180111 chr17:38180142-38180150
8	TFAP2C	chr17:38179537-38180274	Hela-S3	cervix:	n/a	chr17:38179755-38179770 chr17:38180072-38180087
9	POLR2A	chr17:38179276-38179908	MCF10A-Er-Src	breast:	n/a	n/a
10	ESR1	chr17:38179571-38179942	ECC-1	luminal epithelium:	n/a	n/a
11	FOS	chr17:38179595-38180341	MCF10A-Er-Src	breast:	n/a	n/a
12	TCF12	chr17:38179675-38180309	A549	lung:	n/a	n/a
13	MYC	chr17:38179285-38180128	MCF10A-Er-Src	breast:	n/a	n/a
14	STAT3	chr17:38179494-38180379	MCF10A-Er-Src	breast:	n/a	chr17:38180099-38180111 chr17:38180142-38180150
15	POLR2A	chr17:38179365-38180383	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr17:38179788-38179803	HUVEC	blood vessel:	n/a	n/a
17	ESR1	chr17:38179393-38180041	ECC-1	luminal epithelium:	n/a	n/a
18	MAZ	chr17:38179791-38179819	Hela-S3	cervix:	n/a	n/a
19	ESR1	chr17:38179502-38180053	ECC-1	luminal epithelium:	n/a	n/a
20	NR3C1	chr17:38179693-38180266	A549	lung:	n/a	n/a
21	GATA3	chr17:38179462-38180249	MCF-7	breast:	n/a	n/a
22	FOS	chr17:38179671-38180298	MCF10A-Er-Src	breast:	n/a	n/a
23	NR2F2	chr17:38179525-38180111	MCF-7	breast:	n/a	n/a
24	EP300	chr17:38179461-38180059	MCF-7	breast:	n/a	n/a
25	STAT3	chr17:38179774-38180387	MCF10A-Er-Src	breast:	n/a	chr17:38180099-38180111 chr17:38180142-38180150
26	CREB1	chr17:38179786-38180214	A549	lung:	n/a	n/a
27	STAT3	chr17:38179576-38180344	MCF10A-Er-Src	breast:	n/a	chr17:38180099-38180111 chr17:38180142-38180150
28	NR3C1	chr17:38179780-38180303	A549	lung:	n/a	n/a
29	FOS	chr17:38179613-38180325	MCF10A-Er-Src	breast:	n/a	n/a
30	STAT3	chr17:38179514-38180380	MCF10A-Er-Src	breast:	n/a	chr17:38180099-38180111 chr17:38180142-38180150
31	FOXA2	chr17:38179750-38180426	A549	lung:	n/a	chr17:38179982-38179994
32	POLR2A	chr17:38179606-38179839	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38178740..38181888-chr17:38181920..38184770,3	K562	blood:
2	chr17:38177803..38180808-chr17:38181920..38184987,3	K562	blood:
3	chr17:38175295..38180645-chr17:38181007..38185256,8	MCF-7	breast:
4	chr17:38179137..38180988-chr17:38255359..38257668,2	MCF-7	breast:
5	chr17:38178218..38182497-chr17:38276428..38279757,5	MCF-7	breast:
6	chr17:38178625..38181576-chr17:38444051..38445917,2	K562	blood:
7	chr17:38177907..38180041-chr17:38332919..38334626,2	MCF-7	breast:
8	chr17:38175071..38177613-chr17:38178105..38180812,3	MCF-7	breast:

Variant related genes	Relation type
MED24	TF binding region
ENSG00000238793	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000126368	Chromatin interaction
ENSG00000108352	Chromatin interaction
ENSG00000188895	Chromatin interaction
ENSG00000094804	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs2227320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2227327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2227328	1.00[AMR][1000 genomes]
rs57870574	1.00[AMR][1000 genomes]
rs58089096	1.00[AMR][1000 genomes]
rs58951919	1.00[AMR][1000 genomes]
rs59309776	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61225269	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7208267	1.00[AMR][1000 genomes]
rs73293503	1.00[AMR][1000 genomes]
rs73295294	1.00[AMR][1000 genomes]
rs73297220	1.00[AMR][1000 genomes]
rs73301225	1.00[AMR][1000 genomes]
rs73301229	1.00[AMR][1000 genomes]
rs73301234	1.00[AMR][1000 genomes]
rs73301238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73305019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73307966	1.00[AMR][1000 genomes]
rs73309981	1.00[AMR][1000 genomes]
rs8079202	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 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	chr17:38166800-38181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr17:38170400-38181600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr17:38171400-38186000	Weak transcription	Small Intestine	intestine
4	chr17:38173000-38181400	Weak transcription	Fetal Kidney	kidney
5	chr17:38173400-38183800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr17:38173400-38192800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:38173600-38180200	Genic enhancers	Fetal Muscle Trunk	muscle
8	chr17:38173600-38180400	Genic enhancers	NHLF	lung
9	chr17:38173600-38182000	Strong transcription	Thymus	Thymus
10	chr17:38173800-38180600	Strong transcription	Brain Anterior Caudate	brain
11	chr17:38173800-38181400	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr17:38173800-38181800	Strong transcription	Primary T cells from cord blood	blood
13	chr17:38173800-38182400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr17:38174000-38192600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr17:38174000-38193800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr17:38174200-38180400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr17:38174200-38180800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr17:38174200-38183200	Strong transcription	Placenta	Placenta
19	chr17:38174200-38183400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr17:38174200-38183400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr17:38174200-38187400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr17:38174400-38183200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr17:38174400-38193200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr17:38174600-38180400	Genic enhancers	Fetal Muscle Leg	muscle
25	chr17:38174600-38181400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr17:38174600-38181800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr17:38174600-38182000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr17:38174800-38181400	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr17:38174800-38192600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr17:38175000-38180600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr17:38175000-38193800	Strong transcription	HepG2	liver
32	chr17:38175200-38181600	Strong transcription	Fetal Thymus	thymus
33	chr17:38175200-38182800	Strong transcription	Brain Angular Gyrus	brain
34	chr17:38175200-38192600	Strong transcription	Fetal Brain Female	brain
35	chr17:38175200-38193200	Strong transcription	Dnd41	blood
36	chr17:38175400-38180200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
37	chr17:38175400-38182200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr17:38175400-38188200	Weak transcription	Fetal Heart	heart
39	chr17:38175600-38181800	Weak transcription	Fetal Brain Male	brain
40	chr17:38175600-38191400	Strong transcription	Brain Hippocampus Middle	brain
41	chr17:38175600-38193200	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr17:38175600-38193200	Strong transcription	Brain Cingulate Gyrus	brain
43	chr17:38175600-38193800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr17:38175800-38182400	Strong transcription	Liver	Liver
45	chr17:38175800-38183400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr17:38175800-38192600	Strong transcription	Brain Germinal Matrix	brain
47	chr17:38176000-38189800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr17:38176000-38192600	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr17:38176000-38195400	Weak transcription	Right Atrium	heart
50	chr17:38176200-38180200	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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