Variant report

Variant	rs1540398
Chromosome Location	chr15:57969330-57969331
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	chr15:57968841-57969341	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57967062..57969940-chr15:57998624..58000773,2	MCF-7	breast:
2	chr15:57968149..57970699-chr15:57997981..57999704,2	K562	blood:

Variant related genes	Relation type
GCOM1	TF binding region
ENSG00000255529	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1346120	0.92[ASN][1000 genomes]
rs1540397	1.00[ASN][1000 genomes]
rs1834487	1.00[AMR][1000 genomes]
rs1946357	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2098891	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2554031	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2733606	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2733610	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2733611	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2733612	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60234362	0.92[AMR][1000 genomes]
rs6493944	1.00[ASN][1000 genomes]
rs7174233	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7181645	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs933839	0.84[AFR][1000 genomes];1.00[AMR][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	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv530682	chr15:57912502-58108285	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1038667	chr15:57933076-58481870	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv542400	chr15:57933076-58481870	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57933400-57982600	Weak transcription	Esophagus	oesophagus
2	chr15:57959600-57982600	Weak transcription	Lung	lung
3	chr15:57960400-57975000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr15:57960800-57985000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:57967000-57970800	Enhancers	Placenta Amnion	Placenta Amnion
6	chr15:57967200-57974800	Weak transcription	Spleen	Spleen
7	chr15:57967800-57976800	Weak transcription	Pancreas	Pancrea
8	chr15:57968000-57972000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:57968200-57971600	Weak transcription	Right Ventricle	heart
10	chr15:57968200-57971800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:57968200-57971800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:57968200-57971800	Weak transcription	NHEK	skin
13	chr15:57968200-57972400	Weak transcription	Stomach Mucosa	stomach
14	chr15:57968200-57976600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr15:57968200-57976800	Weak transcription	Fetal Kidney	kidney
16	chr15:57968200-57983600	Weak transcription	Gastric	stomach
17	chr15:57968400-57970200	Strong transcription	Left Ventricle	heart
18	chr15:57968400-57971800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:57968400-57971800	Weak transcription	HMEC	breast
20	chr15:57968400-57972200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:57968400-57975000	Weak transcription	Fetal Intestine Large	intestine
22	chr15:57968600-57971400	Weak transcription	Adipose Nuclei	Adipose
23	chr15:57968800-57970200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:57969000-57970000	Enhancers	NHDF-Ad	bronchial
25	chr15:57969000-57970600	Strong transcription	Fetal Intestine Small	intestine
26	chr15:57969200-57969800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:57969200-57971600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:57969200-57971600	Weak transcription	Fetal Heart	heart

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