Variant report

Variant	rs12505042
Chromosome Location	chr4:151185111-151185112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11059	0.88[ASW][hapmap];0.81[CEU][hapmap]
rs11929842	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933443	0.85[ASN][1000 genomes]
rs11944163	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12643608	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12644110	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13116727	0.89[ASN][1000 genomes]
rs13121248	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1472842	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1599167	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870515	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1960918	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2290847	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35016840	0.87[ASN][1000 genomes]
rs35370115	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35766906	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62344533	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6535728	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6843403	0.82[EUR][1000 genomes]
rs6850249	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6852979	0.84[ASN][1000 genomes]
rs7653994	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7654538	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657477	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677474	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7677475	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7685302	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026797	chr4:150246932-151217137	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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
6	nsv880257	chr4:151170387-151231371	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv880258	chr4:151171082-151190804	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12505042	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151160000-151185400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr4:151166400-151199000	Weak transcription	Gastric	stomach
3	chr4:151170000-151187000	Weak transcription	NH-A	brain
4	chr4:151170000-151199000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr4:151171200-151186800	Weak transcription	Pancreas	Pancrea
6	chr4:151172000-151185400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:151172800-151185400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:151172800-151188200	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr4:151172800-151201600	Weak transcription	GM12878-XiMat	blood
10	chr4:151173200-151192000	Weak transcription	Fetal Brain Male	brain
11	chr4:151173400-151201400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:151173800-151186800	Weak transcription	Aorta	Aorta
13	chr4:151175000-151185400	Weak transcription	NHLF	lung
14	chr4:151175400-151188000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr4:151175800-151186800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:151175800-151186800	Weak transcription	Ovary	ovary
17	chr4:151176400-151202800	Weak transcription	Psoas Muscle	Psoas
18	chr4:151176600-151185400	Weak transcription	Adipose Nuclei	Adipose
19	chr4:151177000-151185200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr4:151178000-151186800	Weak transcription	Thymus	Thymus
21	chr4:151178000-151193200	Weak transcription	Fetal Lung	lung
22	chr4:151178200-151185200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr4:151178200-151185800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:151178200-151190800	Weak transcription	Small Intestine	intestine
25	chr4:151178200-151192800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr4:151178200-151193000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:151178200-151204200	Weak transcription	Colonic Mucosa	Colon
28	chr4:151178400-151186200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:151178400-151187000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:151178400-151187000	Weak transcription	A549	lung
31	chr4:151178400-151187400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:151178400-151192800	Weak transcription	Lung	lung
33	chr4:151178400-151201400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:151178400-151201600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:151178400-151208600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr4:151178800-151186800	Weak transcription	Liver	Liver
37	chr4:151178800-151191800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:151179400-151186600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr4:151179600-151186000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr4:151179600-151186600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr4:151179600-151186800	Weak transcription	Stomach Mucosa	stomach
42	chr4:151180000-151186600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr4:151180000-151198800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr4:151180200-151197800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr4:151180400-151186200	Weak transcription	NHEK	skin
46	chr4:151180400-151201200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:151180600-151185400	Weak transcription	Fetal Intestine Large	intestine
48	chr4:151181200-151195400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:151181400-151191200	Weak transcription	Brain Substantia Nigra	brain
50	chr4:151181400-151193000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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