Variant report

Variant	rs56109937
Chromosome Location	chr8:52808934-52808935
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:52807403..52809441-chr8:52809988..52811800,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PXDNL-1	chr8:52808751-52808934	ENSG00000253475.1

Variant related genes	Relation type
ENSG00000168300	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10104555	0.86[EUR][1000 genomes]
rs10106132	0.81[EUR][1000 genomes]
rs10106734	1.00[EUR][1000 genomes]
rs10111727	0.86[EUR][1000 genomes]
rs11990932	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11992330	0.85[EUR][1000 genomes]
rs16916958	0.86[EUR][1000 genomes]
rs1996261	0.81[EUR][1000 genomes]
rs28829739	0.81[EUR][1000 genomes]
rs4242473	0.81[EUR][1000 genomes]
rs4242477	0.81[EUR][1000 genomes]
rs4242478	0.93[EUR][1000 genomes]
rs4257997	0.81[EUR][1000 genomes]
rs4305894	0.93[EUR][1000 genomes]
rs4418330	0.93[EUR][1000 genomes]
rs4500071	0.93[EUR][1000 genomes]
rs4518654	0.93[EUR][1000 genomes]
rs4873599	0.81[EUR][1000 genomes]
rs4873600	0.93[EUR][1000 genomes]
rs4873601	0.93[EUR][1000 genomes]
rs4873605	0.93[EUR][1000 genomes]
rs4873612	1.00[EUR][1000 genomes]
rs55730191	0.86[EUR][1000 genomes]
rs55791360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56034922	0.86[EUR][1000 genomes]
rs56105709	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs56150121	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6473659	0.81[EUR][1000 genomes]
rs6473663	0.93[EUR][1000 genomes]
rs6997032	0.81[EUR][1000 genomes]
rs6997972	1.00[EUR][1000 genomes]
rs7000570	0.93[EUR][1000 genomes]
rs73583635	0.86[EUR][1000 genomes]
rs73583640	0.86[EUR][1000 genomes]
rs73592250	0.86[EUR][1000 genomes]
rs7820936	0.93[EUR][1000 genomes]
rs7845506	0.86[EUR][1000 genomes]
rs9643787	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv831316	chr8:52660353-52842928	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 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	chr8:52771800-52810800	Weak transcription	Esophagus	oesophagus
2	chr8:52779400-52809000	Weak transcription	Fetal Kidney	kidney
3	chr8:52782200-52809600	Weak transcription	Aorta	Aorta
4	chr8:52797400-52809000	Weak transcription	HMEC	breast
5	chr8:52797400-52809600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr8:52797400-52809600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr8:52797400-52810800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:52798000-52810800	Weak transcription	Spleen	Spleen
9	chr8:52799600-52809800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr8:52800000-52809000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr8:52801600-52810200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr8:52801800-52809600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr8:52801800-52810800	Weak transcription	Gastric	stomach
14	chr8:52802400-52810000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr8:52803400-52809800	Weak transcription	Colonic Mucosa	Colon
16	chr8:52803400-52810200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:52804000-52809200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr8:52804000-52809400	Weak transcription	Fetal Muscle Leg	muscle
19	chr8:52804000-52809600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr8:52804000-52809600	Weak transcription	Fetal Intestine Large	intestine
21	chr8:52804000-52809600	Weak transcription	Right Atrium	heart
22	chr8:52804200-52809800	Weak transcription	Left Ventricle	heart
23	chr8:52804200-52810400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr8:52804200-52810400	Weak transcription	Lung	lung
25	chr8:52805000-52809200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr8:52805200-52809800	Weak transcription	Psoas Muscle	Psoas
27	chr8:52805800-52810000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr8:52806200-52809600	Enhancers	HepG2	liver
29	chr8:52806200-52810000	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr8:52806400-52809200	Genic enhancers	Dnd41	blood
31	chr8:52806400-52809600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr8:52806400-52809800	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr8:52806400-52809800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr8:52806400-52810200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr8:52806600-52810000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr8:52806600-52810000	Enhancers	Small Intestine	intestine
37	chr8:52806800-52809600	Enhancers	Fetal Intestine Small	intestine
38	chr8:52806800-52809600	Weak transcription	Stomach Mucosa	stomach
39	chr8:52807000-52809000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr8:52807000-52809200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr8:52807000-52809600	Weak transcription	Brain Angular Gyrus	brain
42	chr8:52807200-52809000	Weak transcription	Ovary	ovary
43	chr8:52807200-52809000	Enhancers	HUVEC	blood vessel
44	chr8:52807200-52809200	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr8:52807200-52809200	Enhancers	NHDF-Ad	bronchial
46	chr8:52807200-52809400	Enhancers	Primary T cells from cord blood	blood
47	chr8:52807200-52810400	Weak transcription	Placenta	Placenta
48	chr8:52807400-52809000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr8:52807400-52809000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr8:52807600-52809000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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