Variant report

Variant	rs3169574
Chromosome Location	chr17:38077485-38077486
allele	A/C/G/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:2)
LncRNA
region (count:1)
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	chr17:38076211-38078398	GM12878	blood:	n/a	n/a
2	PML	chr17:38076716-38077920	GM12878	blood:	n/a	n/a
3	POLR2A	chr17:38076917-38078255	K562	blood:	n/a	n/a
4	POLR2A	chr17:38076141-38078642	HepG2	liver:	n/a	n/a
5	MTA3	chr17:38076294-38078220	GM12878	blood:	n/a	n/a
6	POLR2A	chr17:38077428-38077782	GM12892	blood:	n/a	n/a
7	ELF1	chr17:38077426-38077907	GM12878	blood:	n/a	n/a
8	HEY1	chr17:38076113-38078575	HepG2	liver:	n/a	n/a
9	FOXA1	chr17:38076906-38077496	HepG2	liver:	n/a	n/a
10	EBF1	chr17:38077468-38077972	GM12878	blood:	n/a	n/a
11	RXRA	chr17:38077101-38077517	HepG2	liver:	n/a	n/a
12	POLR2A	chr17:38077456-38077835	GM12891	blood:	n/a	n/a
13	MYBL2	chr17:38076655-38077527	HepG2	liver:	n/a	n/a
14	POLR2A	chr17:38077260-38078488	HepG2	liver:	n/a	n/a
15	STAT3	chr17:38077306-38077506	GM12878	blood:	n/a	n/a
16	POLR2A	chr17:38077360-38077728	HepG2	liver:	n/a	n/a
17	POLR2A	chr17:38076211-38078024	GM12892	blood:	n/a	n/a
18	POU2F2	chr17:38076641-38077591	GM12878	blood:	n/a	n/a
19	POLR2A	chr17:38077416-38077929	GM12892	blood:	n/a	n/a
20	POLR2A	chr17:38077433-38077489	HepG2	liver:	n/a	n/a
21	FOXA1	chr17:38077035-38077512	HepG2	liver:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38073305..38078163-chr17:38135913..38140017,5	K562	blood:
2	chr17:38073305..38078633-chr17:38135671..38140017,6	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GSDMB-1	chr17:38077296-38077570	NONHSAT053494

No data

Variant related genes	Relation type
GSDMB	TF binding region
ENSG00000108344	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1453560	0.82[EUR][1000 genomes]
rs17676923	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2123685	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3169572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35104165	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35336365	0.93[EUR][1000 genomes]
rs3859186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38057800-38077600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr17:38058200-38077800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr17:38059000-38082400	Weak transcription	Psoas Muscle	Psoas
4	chr17:38060400-38081600	Weak transcription	Fetal Brain Male	brain
5	chr17:38061800-38081000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr17:38062800-38078200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr17:38066600-38078000	Weak transcription	Fetal Heart	heart
8	chr17:38068800-38077600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr17:38070200-38077600	Weak transcription	Ovary	ovary
10	chr17:38071800-38077600	Weak transcription	HUVEC	blood vessel
11	chr17:38072800-38080000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr17:38073000-38078400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr17:38073000-38079600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr17:38073000-38080000	Strong transcription	Osteobl	bone
15	chr17:38073200-38079200	Strong transcription	Fetal Muscle Leg	muscle
16	chr17:38073200-38080200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr17:38073800-38078800	Weak transcription	Fetal Kidney	kidney
18	chr17:38073800-38081200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr17:38074200-38077600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr17:38074200-38077600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr17:38074200-38080800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr17:38074200-38080800	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr17:38074200-38080800	Strong transcription	Fetal Brain Female	brain
24	chr17:38074200-38081000	Genic enhancers	Fetal Thymus	thymus
25	chr17:38074400-38080400	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr17:38074400-38080400	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr17:38074400-38080800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr17:38074400-38080800	Weak transcription	Small Intestine	intestine
29	chr17:38074400-38082200	Genic enhancers	Placenta	Placenta
30	chr17:38074400-38082400	Weak transcription	Hela-S3	cervix
31	chr17:38074600-38080200	Strong transcription	Left Ventricle	heart
32	chr17:38074800-38080200	Strong transcription	Fetal Stomach	stomach
33	chr17:38075000-38081200	Strong transcription	Brain Germinal Matrix	brain
34	chr17:38075000-38081400	Genic enhancers	Fetal Intestine Large	intestine
35	chr17:38075200-38078600	Genic enhancers	Spleen	Spleen
36	chr17:38075200-38079800	Genic enhancers	Liver	Liver
37	chr17:38075200-38080000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr17:38075200-38080200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr17:38075200-38080400	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr17:38075200-38080800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
41	chr17:38075200-38081000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr17:38075400-38077800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr17:38075400-38078200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr17:38075400-38078600	Weak transcription	HMEC	breast
45	chr17:38075400-38079600	Strong transcription	Right Ventricle	heart
46	chr17:38075400-38080000	Strong transcription	Lung	lung
47	chr17:38075400-38080200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr17:38075400-38080200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr17:38075400-38080200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr17:38075400-38080200	Strong transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links