Variant report

Variant	rs6504041
Chromosome Location	chr17:59465600-59465601
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	RAD21	chr17:59464232-59473165	MCF-7	breast:	n/a	chr17:59469180-59469190 chr17:59469147-59469157 chr17:59471166-59471180 chr17:59467970-59467984 chr17:59467474-59467493 chr17:59471160-59471173 chr17:59468503-59468516 chr17:59465088-59465102 chr17:59471168-59471187 chr17:59464507-59464519 chr17:59471513-59471526 chr17:59470903-59470917 chr17:59466182-59466196 chr17:59472703-59472713 chr17:59469179-59469192
2	POLR2A	chr17:59464382-59468266	ProgFib	skin:	n/a	n/a
3	TEAD4	chr17:59464268-59466084	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
2	chr17:59464623..59466893-chr7:2561547..2564361,2	MCF-7	breast:
3	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:

Variant related genes	Relation type
BCAS3	TF binding region
ENSG00000124243	Chromatin interaction
ENSG00000106003	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs16945213	1.00[EUR][1000 genomes]
rs57045595	1.00[EUR][1000 genomes]
rs58582622	1.00[EUR][1000 genomes]
rs60549606	1.00[EUR][1000 genomes]
rs6504040	1.00[EUR][1000 genomes]
rs7211905	1.00[EUR][1000 genomes]
rs7214625	1.00[EUR][1000 genomes]
rs7219765	1.00[EUR][1000 genomes]
rs73322588	1.00[EUR][1000 genomes]
rs73991905	1.00[EUR][1000 genomes]
rs73991907	1.00[EUR][1000 genomes]
rs73991919	1.00[EUR][1000 genomes]
rs9891905	1.00[EUR][1000 genomes]
rs9911414	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065939	chr17:59283350-59517730	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	331 gene(s)	inside rSNPs	diseases
2	nsv833505	chr17:59323466-59518007	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	326 gene(s)	inside rSNPs	diseases
3	nsv833506	chr17:59362377-59562984	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
4	nsv518130	chr17:59456589-59491281	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	265 gene(s)	inside rSNPs	diseases
5	esv1796927	chr17:59460119-59495319	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	270 gene(s)	inside rSNPs	diseases
6	nsv908663	chr17:59464069-59521310	Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	278 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59438200-59470800	Weak transcription	Esophagus	oesophagus
2	chr17:59444400-59467000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr17:59444600-59473400	Weak transcription	Right Atrium	heart
4	chr17:59447000-59473400	Weak transcription	Pancreas	Pancrea
5	chr17:59447200-59467000	Weak transcription	Gastric	stomach
6	chr17:59447400-59466800	Weak transcription	Fetal Intestine Small	intestine
7	chr17:59451600-59467000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr17:59455600-59466800	Weak transcription	Lung	lung
9	chr17:59456200-59467000	Weak transcription	Aorta	Aorta
10	chr17:59458000-59467000	Weak transcription	Osteobl	bone
11	chr17:59458600-59467200	Weak transcription	Fetal Kidney	kidney
12	chr17:59458800-59466600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr17:59459200-59466800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr17:59459200-59469400	Weak transcription	Brain Hippocampus Middle	brain
15	chr17:59461000-59467000	Weak transcription	Left Ventricle	heart
16	chr17:59461400-59466800	Weak transcription	Spleen	Spleen
17	chr17:59462000-59466800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr17:59462000-59466800	Weak transcription	NHLF	lung
19	chr17:59462400-59466800	Weak transcription	Adipose Nuclei	Adipose
20	chr17:59462400-59471600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr17:59462600-59470800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr17:59463000-59466800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr17:59463200-59469400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr17:59463800-59467200	Enhancers	HepG2	liver
25	chr17:59464000-59466800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr17:59464000-59467200	Weak transcription	NHDF-Ad	bronchial
27	chr17:59464000-59471000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr17:59464000-59474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr17:59464800-59465600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr17:59464800-59466600	Weak transcription	Fetal Lung	lung
31	chr17:59465000-59466800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr17:59465200-59465600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
33	chr17:59465400-59465600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr17:59465400-59466200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr17:59465400-59466800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr17:59465400-59468000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr17:59465600-59465800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr17:59465600-59468400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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