Variant report

Variant	rs565385
Chromosome Location	chr4:48349414-48349415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48342295..48345695-chr4:48348596..48352687,7	MCF-7	breast:
2	chr4:48342958..48345732-chr4:48348835..48351792,2	MCF-7	breast:
3	chr4:48337400..48346343-chr4:48347805..48355704,14	K562	blood:
4	chr4:48348136..48350109-chr4:48359251..48361101,2	K562	blood:

Variant related genes	Relation type
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs13101954	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13142082	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1352432	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1466631	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1844149	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029347	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291476	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28840724	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34239305	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34380340	0.80[AFR][1000 genomes]
rs35265097	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35963236	0.92[AFR][1000 genomes]
rs36157430	0.81[EUR][1000 genomes]
rs366168	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs375259	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs384885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs393338	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3943122	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs397257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs401463	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs409911	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694894	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4695374	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56089943	0.80[AFR][1000 genomes]
rs565234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62309450	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62311260	0.92[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6447629	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66671150	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6819696	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6819847	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73246021	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73246023	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[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	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48344800-48352200	Weak transcription	Pancreas	Pancrea
2	chr4:48344800-48354400	Weak transcription	Esophagus	oesophagus
3	chr4:48344800-48362400	Weak transcription	Gastric	stomach
4	chr4:48345000-48350000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr4:48345400-48350400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:48345800-48353600	Weak transcription	Spleen	Spleen
7	chr4:48345800-48356000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:48345800-48356600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr4:48346000-48350000	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr4:48346000-48350800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:48346000-48351200	Weak transcription	A549	lung
12	chr4:48346000-48353000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr4:48346000-48362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:48346200-48350600	Weak transcription	Brain Anterior Caudate	brain
15	chr4:48346200-48352200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr4:48346200-48354600	Weak transcription	Fetal Intestine Small	intestine
17	chr4:48346200-48356200	Weak transcription	Fetal Thymus	thymus
18	chr4:48346200-48356600	Weak transcription	HUVEC	blood vessel
19	chr4:48346200-48358400	Weak transcription	Small Intestine	intestine
20	chr4:48346200-48362400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:48346400-48350200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr4:48346400-48361200	Weak transcription	Thymus	Thymus
23	chr4:48346600-48349600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr4:48346600-48350000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:48346600-48354800	Weak transcription	Primary B cells from cord blood	blood
26	chr4:48346600-48371000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr4:48347000-48352200	Enhancers	Primary T cells from cord blood	blood
28	chr4:48347000-48354600	Weak transcription	Aorta	Aorta
29	chr4:48347200-48359600	Weak transcription	Fetal Stomach	stomach
30	chr4:48347400-48350800	Weak transcription	Fetal Brain Male	brain
31	chr4:48347400-48352200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr4:48347400-48353600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:48347400-48353800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr4:48347400-48354600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:48347400-48362200	Weak transcription	Brain Substantia Nigra	brain
36	chr4:48347400-48362200	Weak transcription	NHLF	lung
37	chr4:48347600-48349800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr4:48347600-48349800	Weak transcription	Liver	Liver
39	chr4:48347600-48350000	Weak transcription	Brain Hippocampus Middle	brain
40	chr4:48347600-48351200	Weak transcription	Brain Angular Gyrus	brain
41	chr4:48347600-48351800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr4:48347600-48351800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr4:48347600-48352800	Weak transcription	Fetal Kidney	kidney
44	chr4:48347600-48353000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr4:48347600-48354600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:48347600-48365000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:48348200-48350800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:48348200-48353600	Weak transcription	Dnd41	blood
49	chr4:48348400-48349600	Enhancers	Adipose Nuclei	Adipose
50	chr4:48348400-48352000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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