Variant report

Variant	rs10015104
Chromosome Location	chr4:151484685-151484686
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10006803	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10012087	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10018886	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10022844	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10030673	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12649589	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13104084	0.85[ASN][1000 genomes]
rs13124512	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13127921	0.84[ASN][1000 genomes]
rs13134428	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13145262	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13150736	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13151692	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1394496	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1504785	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1566867	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1857750	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1976494	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4380502	0.81[ASN][1000 genomes]
rs4413387	0.81[ASN][1000 genomes]
rs7690080	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs991529	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9993229	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9994153	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9999828	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv817540	chr4:151228965-151858609	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv869051	chr4:151347901-151737781	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1024820	chr4:151364078-151943561	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1018942	chr4:151423295-151556444	ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv537301	chr4:151423295-151556444	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10015104	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151470400-151503600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr4:151472000-151490000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:151472000-151501400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:151472600-151500200	Weak transcription	Aorta	Aorta
5	chr4:151473400-151486000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:151473400-151491200	Weak transcription	Ovary	ovary
7	chr4:151474200-151489600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr4:151474800-151486400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:151475200-151486200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr4:151475400-151486000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:151475400-151486200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:151475400-151486200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr4:151475400-151486400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr4:151475600-151486000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr4:151475600-151486000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:151475600-151486000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:151477200-151486000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:151477200-151486400	Weak transcription	Fetal Intestine Small	intestine
19	chr4:151477200-151502400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr4:151478400-151486200	Weak transcription	Primary B cells from cord blood	blood
21	chr4:151478800-151489600	Weak transcription	A549	lung
22	chr4:151479200-151486200	Weak transcription	Primary T cells from cord blood	blood
23	chr4:151479400-151490200	Weak transcription	K562	blood
24	chr4:151479400-151500800	Weak transcription	Lung	lung
25	chr4:151479600-151501800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr4:151480600-151500800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:151481200-151500400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr4:151482000-151491000	Weak transcription	Fetal Thymus	thymus
29	chr4:151482800-151488200	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:151484200-151486000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr4:151484400-151486000	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links