Variant report

Variant	rs55998463
Chromosome Location	chr4:151412346-151412347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:151411373..151413789-chr4:151414045..151416361,2	K562	blood:
2	chr4:151411570..151413992-chr4:151416571..151418811,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11721723	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11722416	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726007	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11727758	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11727995	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11729560	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11731650	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11737261	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11931161	0.85[EUR][1000 genomes]
rs11932482	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11936019	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11936496	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11936646	0.84[EUR][1000 genomes]
rs11937036	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11940101	0.84[EUR][1000 genomes]
rs17504602	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17504868	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17588965	0.84[EUR][1000 genomes]
rs17589182	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17589398	0.82[ASN][1000 genomes]
rs2271043	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2292122	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36187100	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413388	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4419457	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4593110	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696185	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696458	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55875525	0.84[EUR][1000 genomes]
rs55977492	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56671775	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57452017	0.84[ASN][1000 genomes]
rs58633621	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62344660	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62344663	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62344664	0.95[ASN][1000 genomes]
rs62344694	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62344697	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62344699	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62344702	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62344705	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62344742	0.84[ASN][1000 genomes]
rs62348579	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62348580	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62348581	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72734459	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72734461	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72734468	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72734475	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72734477	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72734478	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72734489	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72734495	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7687343	0.83[EUR][1000 genomes]
rs7690365	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	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
2	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
3	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
4	nsv830112	chr4:151243801-151431771	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55998463	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151364600-151414800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr4:151374400-151419000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:151377000-151412400	Weak transcription	Liver	Liver
4	chr4:151382400-151422400	Weak transcription	Adipose Nuclei	Adipose
5	chr4:151385400-151442200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr4:151387600-151412600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:151387600-151419000	Weak transcription	K562	blood
8	chr4:151387800-151423000	Weak transcription	Colon Smooth Muscle	Colon
9	chr4:151392200-151413000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:151392200-151414800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:151392200-151424400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:151395200-151416800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:151395400-151424000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:151398600-151415000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:151399600-151413000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:151400000-151434200	Weak transcription	Primary T cells from cord blood	blood
17	chr4:151400400-151422000	Weak transcription	Osteobl	bone
18	chr4:151406200-151416200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:151407000-151412600	Weak transcription	Fetal Kidney	kidney
20	chr4:151408400-151413200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr4:151408400-151413800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr4:151408400-151422200	Weak transcription	Primary B cells from cord blood	blood
23	chr4:151408800-151412600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:151409000-151422000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:151409000-151456600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr4:151410000-151444400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:151411200-151412400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr4:151411600-151412800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:151412000-151413600	Weak transcription	GM12878-XiMat	blood
30	chr4:151412000-151424200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr4:151412200-151413800	Weak transcription	Fetal Intestine Large	intestine
32	chr4:151412200-151414000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:151412200-151416600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr4:151412200-151424200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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