Variant report

Variant	rs7654538
Chromosome Location	chr4:151201635-151201636
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:151199693..151202528-chr4:151202703..151205014,2	K562	blood:

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

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

rs_ID	r²[population]
rs11929842	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933443	0.85[ASN][1000 genomes]
rs11944163	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12505042	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643608	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12644110	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13116727	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13121248	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1472842	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1599167	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870515	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1960918	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2290847	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35016840	0.87[ASN][1000 genomes]
rs35370115	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35766906	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62344533	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6535728	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6850249	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6852979	0.84[ASN][1000 genomes]
rs7653994	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7657477	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677474	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7677475	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7685302	0.94[AMR][1000 genomes];0.98[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7654538	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151176400-151202800	Weak transcription	Psoas Muscle	Psoas
2	chr4:151178200-151204200	Weak transcription	Colonic Mucosa	Colon
3	chr4:151178400-151208600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:151181400-151201800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr4:151181600-151202000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr4:151181600-151202000	Weak transcription	Fetal Kidney	kidney
7	chr4:151181600-151203400	Weak transcription	Right Ventricle	heart
8	chr4:151181800-151209000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr4:151182600-151208000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:151184800-151209200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr4:151185000-151202000	Weak transcription	K562	blood
12	chr4:151186200-151208000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:151186400-151204800	Weak transcription	Placenta	Placenta
14	chr4:151187600-151202000	Weak transcription	Left Ventricle	heart
15	chr4:151187600-151206000	Weak transcription	Dnd41	blood
16	chr4:151187800-151202400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr4:151190200-151204600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr4:151191400-151245200	Weak transcription	Small Intestine	intestine
19	chr4:151192400-151232800	Weak transcription	Brain Substantia Nigra	brain
20	chr4:151193400-151208400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:151193600-151203000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr4:151193600-151210200	Weak transcription	HepG2	liver
23	chr4:151195200-151205000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:151197200-151209400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:151197800-151206800	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr4:151198200-151208600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr4:151198400-151204400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr4:151198400-151204600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:151198400-151204600	Strong transcription	Duodenum Mucosa	Duodenum
30	chr4:151198400-151205000	Strong transcription	Primary B cells from cord blood	blood
31	chr4:151198400-151209000	Strong transcription	Primary T cells from cord blood	blood
32	chr4:151198600-151204600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr4:151198600-151205200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr4:151198600-151207200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr4:151198800-151204600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr4:151198800-151205400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:151199000-151205000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr4:151199000-151205800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr4:151199200-151202400	Weak transcription	Gastric	stomach
40	chr4:151199200-151203000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:151199200-151203000	Weak transcription	Fetal Muscle Leg	muscle
42	chr4:151199200-151206800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr4:151199200-151208000	Weak transcription	Fetal Lung	lung
44	chr4:151199400-151202800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr4:151199600-151202400	Weak transcription	Adipose Nuclei	Adipose
46	chr4:151199600-151203200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:151199800-151201800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr4:151199800-151201800	Weak transcription	Ovary	ovary
49	chr4:151199800-151201800	Weak transcription	Thymus	Thymus
50	chr4:151199800-151201800	Weak transcription	Spleen	Spleen

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