Variant report

Variant	rs397257
Chromosome Location	chr4:48351096-48351097
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48350227..48353162-chr4:48356080..48357994,2	K562	blood:
2	chr4:48349775..48352299-chr4:48353081..48355903,3	K562	blood:
3	chr4:48342295..48345695-chr4:48348596..48352687,7	MCF-7	breast:
4	chr4:48342958..48345732-chr4:48348835..48351792,2	MCF-7	breast:
5	chr4:48337400..48346343-chr4:48347805..48355704,14	K562	blood:
6	chr4:48328527..48330606-chr4:48349745..48351670,2	K562	blood:
7	chr4:48346882..48348699-chr4:48349922..48352007,2	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];0.94[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];0.91[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]
rs401463	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs409911	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.97[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:95 , 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	chr4:48345800-48353600	Weak transcription	Spleen	Spleen
5	chr4:48345800-48356000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:48345800-48356600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr4:48346000-48351200	Weak transcription	A549	lung
8	chr4:48346000-48353000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr4:48346000-48362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:48346200-48352200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:48346200-48354600	Weak transcription	Fetal Intestine Small	intestine
12	chr4:48346200-48356200	Weak transcription	Fetal Thymus	thymus
13	chr4:48346200-48356600	Weak transcription	HUVEC	blood vessel
14	chr4:48346200-48358400	Weak transcription	Small Intestine	intestine
15	chr4:48346200-48362400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:48346400-48361200	Weak transcription	Thymus	Thymus
17	chr4:48346600-48354800	Weak transcription	Primary B cells from cord blood	blood
18	chr4:48346600-48371000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr4:48347000-48352200	Enhancers	Primary T cells from cord blood	blood
20	chr4:48347000-48354600	Weak transcription	Aorta	Aorta
21	chr4:48347200-48359600	Weak transcription	Fetal Stomach	stomach
22	chr4:48347400-48352200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr4:48347400-48353600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr4:48347400-48353800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:48347400-48354600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:48347400-48362200	Weak transcription	Brain Substantia Nigra	brain
27	chr4:48347400-48362200	Weak transcription	NHLF	lung
28	chr4:48347600-48351200	Weak transcription	Brain Angular Gyrus	brain
29	chr4:48347600-48351800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:48347600-48351800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr4:48347600-48352800	Weak transcription	Fetal Kidney	kidney
32	chr4:48347600-48353000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr4:48347600-48354600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:48347600-48365000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:48348200-48353600	Weak transcription	Dnd41	blood
36	chr4:48348400-48352000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:48348600-48353000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr4:48348600-48353400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr4:48348600-48362400	Weak transcription	Fetal Lung	lung
40	chr4:48348800-48355800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:48348800-48358200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:48348800-48363000	Weak transcription	Hela-S3	cervix
43	chr4:48348800-48371000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr4:48349000-48356600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:48349000-48358400	Weak transcription	HSMM	muscle
46	chr4:48349200-48352200	Weak transcription	Fetal Heart	heart
47	chr4:48349200-48352200	Weak transcription	NHEK	skin
48	chr4:48349200-48352400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:48349200-48353400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr4:48349200-48354600	Weak transcription	K562	blood

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