Variant report

Variant	rs3749574
Chromosome Location	chr4:151207127-151207128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10520053	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1080195	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11059	0.87[CEU][hapmap]
rs11728745	0.86[AFR][1000 genomes]
rs11734641	0.86[AFR][1000 genomes]
rs11734677	0.89[GIH][hapmap]
rs11734774	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11737450	0.86[AFR][1000 genomes]
rs11940101	1.00[ASW][hapmap]
rs1507190	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1507191	0.89[GIH][hapmap];0.81[MEX][hapmap]
rs17503902	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17503964	0.89[GIH][hapmap];0.81[MEX][hapmap]
rs17504117	0.85[AMR][1000 genomes]
rs17588356	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17588629	0.82[AMR][1000 genomes]
rs1824406	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2056457	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2085722	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290846	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35750119	0.86[AFR][1000 genomes]
rs4370117	1.00[ASW][hapmap]
rs4696084	0.86[AFR][1000 genomes]
rs4696299	0.86[AFR][1000 genomes]
rs4696646	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696651	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4696659	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696660	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55728314	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55889963	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56004102	0.86[AFR][1000 genomes]
rs56169929	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56398631	0.86[AFR][1000 genomes]
rs58138000	0.82[AMR][1000 genomes]
rs59435073	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs59713336	0.82[AMR][1000 genomes]
rs60459852	0.82[AMR][1000 genomes]
rs61269060	0.86[AFR][1000 genomes]
rs62344508	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62346985	0.82[AMR][1000 genomes]
rs62346990	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6817154	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834124	0.82[AMR][1000 genomes]
rs6852279	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72734403	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7656639	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657457	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686693	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs999784	0.81[EUR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3749574	LRBA	Cis_1M	lymphoblastoid	RTeQTL
rs3749574	LRBA	cis	normal skin	skin_eQTL
rs3749574	DCLK2	cis	parietal	SCAN
rs3749574	FZD3	trans	parietal	SCAN
rs3749574	ATP2B1	trans	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151178400-151208600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:151181800-151209000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr4:151182600-151208000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr4:151184800-151209200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:151186200-151208000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:151191400-151245200	Weak transcription	Small Intestine	intestine
7	chr4:151192400-151232800	Weak transcription	Brain Substantia Nigra	brain
8	chr4:151193400-151208400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:151193600-151210200	Weak transcription	HepG2	liver
10	chr4:151197200-151209400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:151198200-151208600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr4:151198400-151209000	Strong transcription	Primary T cells from cord blood	blood
13	chr4:151198600-151207200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr4:151199200-151208000	Weak transcription	Fetal Lung	lung
15	chr4:151201200-151207200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:151201200-151207600	Strong transcription	Fetal Intestine Large	intestine
17	chr4:151202000-151208400	Weak transcription	Fetal Heart	heart
18	chr4:151202200-151207400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr4:151202200-151207400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:151202200-151207600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:151202200-151208600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:151202200-151208600	Weak transcription	Esophagus	oesophagus
23	chr4:151202200-151208800	Weak transcription	Ovary	ovary
24	chr4:151202200-151210000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:151202200-151213200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:151202200-151218000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:151202400-151210400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:151202600-151208200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:151202600-151210600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr4:151202600-151213200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:151202800-151210000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr4:151202800-151223800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:151203600-151208600	Weak transcription	Thymus	Thymus
34	chr4:151203600-151218400	Weak transcription	Fetal Stomach	stomach
35	chr4:151203800-151208000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr4:151203800-151208200	Weak transcription	Left Ventricle	heart
37	chr4:151203800-151208600	Weak transcription	Gastric	stomach
38	chr4:151203800-151211000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:151203800-151244400	Weak transcription	Fetal Thymus	thymus
40	chr4:151204000-151208800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:151204000-151211000	Weak transcription	Colon Smooth Muscle	Colon
42	chr4:151204000-151223800	Weak transcription	K562	blood
43	chr4:151204000-151244600	Weak transcription	Lung	lung
44	chr4:151204200-151208000	Weak transcription	Fetal Muscle Leg	muscle
45	chr4:151204200-151210600	Weak transcription	Liver	Liver
46	chr4:151204200-151213200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr4:151204400-151208600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:151204400-151208600	Weak transcription	Right Ventricle	heart
49	chr4:151204600-151208400	Weak transcription	Adipose Nuclei	Adipose
50	chr4:151204600-151208600	Weak transcription	Spleen	Spleen

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