Variant report

Variant	rs4543799
Chromosome Location	chr1:10174189-10174190
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10165812..10172888-chr1:10173533..10178071,7	K562	blood:
2	chr1:10172743..10174968-chr1:10175247..10177682,3	K562	blood:

Variant related genes	Relation type
ENSG00000130939	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1074461	0.81[AMR][1000 genomes]
rs10864442	0.83[AFR][1000 genomes]
rs12076922	0.95[GIH][hapmap]
rs1220421	0.95[LWK][hapmap];0.86[MKK][hapmap]
rs2273298	1.00[ASW][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2273299	0.94[ASW][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35316894	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3762290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782924	0.82[AMR][1000 genomes]
rs6667049	0.94[ASW][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6671289	0.90[CEU][hapmap];0.84[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv522629	chr1:10125765-10239197	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4543799	RERE	cis	parietal	SCAN
rs4543799	LZIC	cis	lymphoblastoid	seeQTL
rs4543799	UBE4B	cis	cerebellum	SCAN
rs4543799	LZIC	Cis_1M	lymphoblastoid	RTeQTL
rs4543799	LZIC	cis	Lymphoblastoid	GTEx
rs4543799	KIF1B	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10145400-10189600	Weak transcription	Psoas Muscle	Psoas
2	chr1:10145800-10197000	Weak transcription	Stomach Mucosa	stomach
3	chr1:10154800-10183000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:10158400-10178000	Strong transcription	Primary T cells from cord blood	blood
5	chr1:10160200-10175800	Strong transcription	Fetal Stomach	stomach
6	chr1:10163400-10219000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:10164000-10227400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:10166200-10179200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:10166600-10181200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:10167000-10181800	Weak transcription	A549	lung
11	chr1:10167200-10179200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:10167400-10174200	Weak transcription	HepG2	liver
13	chr1:10167400-10181600	Weak transcription	Fetal Brain Male	brain
14	chr1:10167400-10188400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:10167400-10192600	Weak transcription	Small Intestine	intestine
16	chr1:10167600-10179400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:10167600-10181600	Weak transcription	Right Ventricle	heart
18	chr1:10167600-10190400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:10167600-10207400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:10167800-10184000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:10169000-10178000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:10169000-10179200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:10169000-10179200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:10169000-10182400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:10169200-10175600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:10169200-10175600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:10169200-10175600	Weak transcription	K562	blood
28	chr1:10169200-10175800	Weak transcription	NHDF-Ad	bronchial
29	chr1:10169200-10177000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:10169200-10177400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:10169200-10178000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:10169200-10181600	Weak transcription	HMEC	breast
33	chr1:10169400-10175600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:10169400-10179400	Weak transcription	HSMM	muscle
35	chr1:10169400-10180400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:10169400-10195000	Weak transcription	Aorta	Aorta
37	chr1:10169600-10174600	Weak transcription	Fetal Lung	lung
38	chr1:10169600-10174800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:10169600-10175000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:10169600-10175400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:10169600-10175800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:10169600-10176400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:10169600-10177600	Weak transcription	GM12878-XiMat	blood
44	chr1:10169600-10177800	Weak transcription	NHLF	lung
45	chr1:10169600-10179200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:10169600-10181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:10169600-10181800	Weak transcription	Hela-S3	cervix
48	chr1:10169800-10177400	Weak transcription	NH-A	brain
49	chr1:10169800-10181800	Weak transcription	Fetal Heart	heart
50	chr1:10170000-10176600	Strong transcription	Fetal Intestine Small	intestine

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