Variant report

Variant	rs11729560
Chromosome Location	chr4:151443289-151443290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11721723	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11722416	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11726007	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11727758	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11727995	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11731650	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11737261	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11931161	0.88[EUR][1000 genomes]
rs11932482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11936019	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11936496	0.81[EUR][1000 genomes]
rs11936646	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11937036	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11940101	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17504602	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17504868	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17588965	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17589182	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17589398	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2271043	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2292122	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36187100	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4370117	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs4413388	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4419457	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4593110	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696185	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696458	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55875525	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55977492	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55998463	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56671775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57452017	0.88[ASN][1000 genomes]
rs58633621	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62344660	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62344663	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62344664	0.91[ASN][1000 genomes]
rs62344694	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62344697	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62344699	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62344702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62344705	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62344742	0.88[ASN][1000 genomes]
rs62348579	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62348580	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62348581	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72734459	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72734461	0.81[EUR][1000 genomes]
rs72734468	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72734475	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72734477	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72734478	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72734489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72734495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7687343	0.86[EUR][1000 genomes]
rs7690365	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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	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	esv3445246	chr4:151422396-151447936	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	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
7	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
rs11729560	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151409000-151456600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:151410000-151444400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:151422800-151474600	Weak transcription	Primary B cells from cord blood	blood
4	chr4:151433800-151444200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr4:151435800-151452600	Weak transcription	Primary T cells from cord blood	blood
6	chr4:151436000-151443800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:151436200-151452000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:151440000-151443600	Weak transcription	Fetal Intestine Small	intestine
9	chr4:151440000-151454200	Weak transcription	HSMMtube	muscle
10	chr4:151440200-151472600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:151441200-151454800	Weak transcription	K562	blood
12	chr4:151442000-151452000	Weak transcription	Psoas Muscle	Psoas
13	chr4:151442800-151445200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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