Variant report

Variant	rs58208423
Chromosome Location	chr11:19137941-19137942
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	POLR2A	chr11:19137874-19139543	GM12891	blood:	n/a	n/a
2	POLR2A	chr11:19137842-19139289	GM12892	blood:	n/a	n/a
3	REST	chr11:19137842-19138108	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAZ	chr11:19137866-19139249	GM12878	blood:	n/a	n/a
5	RUNX3	chr11:19137762-19138286	GM12878	blood:	n/a	n/a
6	POLR2A	chr11:19137766-19138281	GM12878	blood:	n/a	n/a
7	RUNX3	chr11:19137748-19138338	GM12878	blood:	n/a	n/a
8	EBF1	chr11:19137790-19138205	GM12878	blood:	n/a	chr11:19137949-19137959 chr11:19137949-19137958 chr11:19137947-19137958
9	SMARCB1	chr11:19137934-19139316	Hela-S3	cervix:	n/a	n/a
10	NRF1	chr11:19137916-19138326	GM12878	blood:	n/a	n/a
11	EP300	chr11:19137845-19138404	GM12878	blood:	n/a	chr11:19138118-19138132 chr11:19138087-19138100
12	TBL1XR1	chr11:19137849-19138989	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:19137938-19139372	GM18526	blood:	n/a	n/a
14	REST	chr11:19137938-19138086	GM12878	blood:	n/a	n/a
15	POLR2A	chr11:19137805-19139313	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:19137821-19139730	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:19137851-19139347	GM12892	blood:	n/a	n/a
18	EBF1	chr11:19137686-19139176	GM12878	blood:	n/a	chr11:19137949-19137959 chr11:19137949-19137958 chr11:19137947-19137958
19	ZNF143	chr11:19137798-19139262	GM12878	blood:	n/a	chr11:19139017-19139036 chr11:19138834-19138844
20	RELA	chr11:19137806-19139501	GM12891	blood:	n/a	n/a
21	MTA3	chr11:19137774-19139105	GM12878	blood:	n/a	n/a
22	POLR2A	chr11:19137914-19138084	GM12878	blood:	n/a	n/a
23	POLR2A	chr11:19137941-19139440	GM18951	blood:	n/a	n/a
24	EBF1	chr11:19137799-19138141	GM12878	blood:	n/a	chr11:19137949-19137959 chr11:19137949-19137958 chr11:19137947-19137958
25	REST	chr11:19137885-19138053	Hela-S3	cervix:	n/a	n/a
26	STAT1	chr11:19137838-19138318	GM12878	blood:	n/a	n/a
27	POLR2A	chr11:19137899-19139406	GM12892	blood:	n/a	n/a
28	TBP	chr11:19137884-19138954	GM12878	blood:	n/a	n/a
29	REST	chr11:19137894-19138112	H1-hESC	embryonic stem cell:	n/a	n/a
30	CHD2	chr11:19137911-19139212	GM12878	blood:	n/a	chr11:19138056-19138066
31	EP300	chr11:19137808-19138262	GM12878	blood:	n/a	chr11:19138118-19138132 chr11:19138087-19138100
32	REST	chr11:19137803-19138239	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:19137492..19139036-chr11:19169967..19172250,2	MCF-7	breast:

Variant related genes	Relation type
ZDHHC13	TF binding region
ENSG00000177054	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11025027	0.86[AFR][1000 genomes]
rs16936075	0.84[ASN][1000 genomes]
rs16936115	0.88[ASN][1000 genomes]
rs3934970	0.87[ASN][1000 genomes]
rs56946079	0.81[ASN][1000 genomes]
rs57666278	0.88[ASN][1000 genomes]
rs59246389	0.89[ASN][1000 genomes]
rs59630455	0.81[ASN][1000 genomes]
rs60304302	0.88[ASN][1000 genomes]
rs60767473	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6483578	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7938838	0.81[AFR][1000 genomes]
rs7941959	0.81[AFR][1000 genomes]
rs7942071	0.81[AFR][1000 genomes]
rs924750	1.00[AMR][1000 genomes];0.91[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	nsv1040805	chr11:19037871-19892803	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv540957	chr11:19037871-19892803	Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:19125000-19138600	Weak transcription	Gastric	stomach
2	chr11:19131600-19138000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr11:19131600-19138000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:19132000-19138000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr11:19132200-19138000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr11:19132800-19138000	Weak transcription	Pancreas	Pancrea
7	chr11:19133400-19138000	Weak transcription	Fetal Brain Female	brain
8	chr11:19133400-19138000	Weak transcription	Fetal Heart	heart
9	chr11:19133600-19138000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr11:19134200-19138200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:19137400-19138200	Enhancers	NHEK	skin
12	chr11:19137800-19138000	Enhancers	H1 Cell Line	embryonic stem cell
13	chr11:19137800-19138000	Enhancers	Primary B cells from cord blood	blood
14	chr11:19137800-19138000	Enhancers	Primary B cells from peripheral blood	blood
15	chr11:19137800-19138000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr11:19137800-19138000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr11:19137800-19138000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr11:19137800-19138000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:19137800-19138000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr11:19137800-19138000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr11:19137800-19138000	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr11:19137800-19138000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:19137800-19138000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr11:19137800-19138000	Enhancers	Brain Anterior Caudate	brain
25	chr11:19137800-19138000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:19137800-19138000	Active TSS	Duodenum Mucosa	Duodenum
27	chr11:19137800-19138000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr11:19137800-19138000	Bivalent Enhancer	A549	lung
29	chr11:19137800-19138000	Enhancers	Dnd41	blood
30	chr11:19137800-19138200	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr11:19137800-19138200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr11:19137800-19138200	Enhancers	Brain Germinal Matrix	brain
33	chr11:19137800-19138200	Enhancers	Right Atrium	heart
34	chr11:19137800-19138400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr11:19137800-19138400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:19137800-19138400	Bivalent Enhancer	Placenta	Placenta
37	chr11:19137800-19138400	Enhancers	Left Ventricle	heart
38	chr11:19137800-19138400	Bivalent Enhancer	Lung	lung
39	chr11:19137800-19138400	Flanking Active TSS	GM12878-XiMat	blood
40	chr11:19137800-19138400	Flanking Bivalent TSS/Enh	HepG2	liver

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