Variant report

Variant	rs71513561
Chromosome Location	chr8:52808608-52808609
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:
2	chr8:52762297..52765279-chr8:52806438..52808911,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PXDNL-1	chr8:52808517-52808615	ENSG00000253475.1

Variant related genes	Relation type
ENSG00000168300	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10101163	0.82[EUR][1000 genomes]
rs10504130	0.98[ASN][1000 genomes]
rs10958300	1.00[ASN][1000 genomes]
rs10958301	1.00[ASN][1000 genomes]
rs10958304	0.81[EUR][1000 genomes]
rs10958305	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11775587	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11775611	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11777016	1.00[ASN][1000 genomes]
rs11777714	1.00[ASN][1000 genomes]
rs11778849	0.98[ASN][1000 genomes]
rs11780040	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781330	0.98[ASN][1000 genomes]
rs11784869	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11785467	0.83[AMR][1000 genomes]
rs11785805	0.96[ASN][1000 genomes]
rs11787229	0.88[ASN][1000 genomes]
rs11787499	0.81[EUR][1000 genomes]
rs12675786	0.98[ASN][1000 genomes]
rs12675907	0.85[ASN][1000 genomes]
rs12676345	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12676780	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12676835	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12677407	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12678639	0.96[ASN][1000 genomes]
rs12679287	0.96[ASN][1000 genomes]
rs12679983	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12680128	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12681203	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12681734	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13265006	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13274159	0.85[AMR][1000 genomes]
rs13275967	0.85[AMR][1000 genomes]
rs13276400	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16916820	0.98[ASN][1000 genomes]
rs16916856	0.98[ASN][1000 genomes]
rs16916865	0.98[ASN][1000 genomes]
rs16916906	1.00[ASN][1000 genomes]
rs16916952	0.81[EUR][1000 genomes]
rs16916961	0.96[ASN][1000 genomes]
rs17212214	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17212256	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17284746	0.96[ASN][1000 genomes]
rs2037138	0.98[ASN][1000 genomes]
rs2037139	1.00[ASN][1000 genomes]
rs2069119	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2176120	1.00[ASN][1000 genomes]
rs34004633	0.85[AMR][1000 genomes]
rs34058697	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34073804	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34213209	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34319820	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34364864	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34372756	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34677273	0.96[ASN][1000 genomes]
rs34780436	0.85[AMR][1000 genomes]
rs34973406	0.98[ASN][1000 genomes]
rs35032384	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35509250	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35603537	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41453644	0.96[ASN][1000 genomes]
rs4242479	0.82[EUR][1000 genomes]
rs4292674	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4321994	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4436115	0.85[AMR][1000 genomes]
rs4534123	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4573262	0.85[AMR][1000 genomes]
rs4598243	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4626585	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57212480	0.98[ASN][1000 genomes]
rs58561048	0.98[ASN][1000 genomes]
rs58583070	0.87[ASN][1000 genomes]
rs59602923	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60153173	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60304457	0.96[ASN][1000 genomes]
rs60796336	0.96[ASN][1000 genomes]
rs61326367	0.87[ASN][1000 genomes]
rs6768	0.82[AMR][1000 genomes]
rs6994203	0.93[ASN][1000 genomes]
rs71513549	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71513552	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71513564	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs763550	0.98[ASN][1000 genomes]
rs9650179	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9650180	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9650305	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9792352	1.00[ASN][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	chr8:52798800-52808800	Weak transcription	Fetal Brain Female	brain
10	chr8:52799600-52809800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr8:52800000-52809000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr8:52801600-52810200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr8:52801800-52809600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr8:52801800-52810800	Weak transcription	Gastric	stomach
15	chr8:52802400-52810000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr8:52803400-52809800	Weak transcription	Colonic Mucosa	Colon
17	chr8:52803400-52810200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr8:52804000-52809200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr8:52804000-52809400	Weak transcription	Fetal Muscle Leg	muscle
20	chr8:52804000-52809600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr8:52804000-52809600	Weak transcription	Fetal Intestine Large	intestine
22	chr8:52804000-52809600	Weak transcription	Right Atrium	heart
23	chr8:52804200-52809800	Weak transcription	Left Ventricle	heart
24	chr8:52804200-52810400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr8:52804200-52810400	Weak transcription	Lung	lung
26	chr8:52805000-52809200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr8:52805200-52809800	Weak transcription	Psoas Muscle	Psoas
28	chr8:52805800-52810000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr8:52806200-52809600	Enhancers	HepG2	liver
30	chr8:52806200-52810000	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr8:52806400-52809200	Genic enhancers	Dnd41	blood
32	chr8:52806400-52809600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr8:52806400-52809800	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr8:52806400-52809800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr8:52806400-52810200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr8:52806600-52810000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr8:52806600-52810000	Enhancers	Small Intestine	intestine
38	chr8:52806800-52809600	Enhancers	Fetal Intestine Small	intestine
39	chr8:52806800-52809600	Weak transcription	Stomach Mucosa	stomach
40	chr8:52807000-52809000	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr8:52807000-52809200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr8:52807000-52809600	Weak transcription	Brain Angular Gyrus	brain
43	chr8:52807200-52809000	Weak transcription	Ovary	ovary
44	chr8:52807200-52809000	Enhancers	HUVEC	blood vessel
45	chr8:52807200-52809200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr8:52807200-52809200	Enhancers	NHDF-Ad	bronchial
47	chr8:52807200-52809400	Enhancers	Primary T cells from cord blood	blood
48	chr8:52807200-52810400	Weak transcription	Placenta	Placenta
49	chr8:52807400-52809000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr8:52807400-52809000	Weak transcription	Rectal Smooth Muscle	rectum

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