Variant report

Variant	rs62346572
Chromosome Location	chr4:151129865-151129866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr4:151129681-151131107	SK-N-SH	brain:	n/a	chr4:151130736-151130748 chr4:151130737-151130750 chr4:151130738-151130748 chr4:151130734-151130753

No.	Distal block	Cell Line	Cell type
1	chr4:151128805..151130494-chr4:151141671..151144389,2	K562	blood:
2	chr1:50273756..50275417-chr4:151127918..151130804,2	MCF-7	breast:
3	chr4:150932709..150934919-chr4:151128696..151130232,2	MCF-7	breast:

Variant related genes	Relation type
RNU7-194P	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12374344	1.00[ASN][1000 genomes]
rs13435901	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2305980	0.82[ASN][1000 genomes]
rs28405622	0.94[ASN][1000 genomes]
rs28468660	0.92[ASN][1000 genomes]
rs4696597	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62346572	LRBA	Cis_1M	lymphoblastoid	RTeQTL
rs62346572	DCLK2	cis	Whole Blood	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151103200-151138000	Weak transcription	NH-A	brain
2	chr4:151108600-151130000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr4:151114200-151154200	Weak transcription	Aorta	Aorta
4	chr4:151120000-151132200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:151122200-151137800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:151123800-151136800	Weak transcription	Fetal Intestine Large	intestine
7	chr4:151124000-151132200	Weak transcription	Right Ventricle	heart
8	chr4:151126200-151130200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr4:151127000-151130000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:151127000-151132600	Enhancers	Brain Germinal Matrix	brain
11	chr4:151127200-151130600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:151128000-151132400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:151128000-151132400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:151128000-151132800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:151128000-151132800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:151128000-151137000	Weak transcription	Brain Angular Gyrus	brain
17	chr4:151128000-151138000	Weak transcription	Brain Substantia Nigra	brain
18	chr4:151128000-151138000	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:151128200-151131000	Enhancers	A549	lung
20	chr4:151128200-151132800	Weak transcription	Osteobl	bone
21	chr4:151128200-151137800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:151128400-151132200	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:151128400-151132200	Weak transcription	Fetal Stomach	stomach
24	chr4:151128400-151133800	Weak transcription	HSMM	muscle
25	chr4:151128400-151138200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:151128600-151130600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:151128600-151131400	Weak transcription	HSMMtube	muscle
28	chr4:151128600-151132400	Weak transcription	Fetal Kidney	kidney
29	chr4:151128600-151132800	Weak transcription	Fetal Lung	lung
30	chr4:151128600-151137800	Weak transcription	Brain Anterior Caudate	brain
31	chr4:151129000-151130600	Enhancers	Brain Hippocampus Middle	brain
32	chr4:151129200-151130000	Weak transcription	Ovary	ovary
33	chr4:151129200-151130400	Weak transcription	Lung	lung
34	chr4:151129200-151131400	Weak transcription	Fetal Brain Female	brain
35	chr4:151129200-151132200	Weak transcription	Right Atrium	heart
36	chr4:151129400-151130200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:151129400-151132400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:151129400-151137600	Weak transcription	Fetal Brain Male	brain
39	chr4:151129600-151130000	Weak transcription	Left Ventricle	heart
40	chr4:151129600-151130800	Enhancers	Adipose Nuclei	Adipose
41	chr4:151129800-151130200	Enhancers	Brain Cingulate Gyrus	brain
42	chr4:151129800-151132200	Weak transcription	Fetal Heart	heart

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