Variant report

Variant	rs12374344
Chromosome Location	chr4:151126725-151126726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10002709	0.82[CEU][hapmap]
rs10520059	1.00[JPT][hapmap]
rs13435901	0.94[ASN][1000 genomes]
rs17026748	1.00[JPT][hapmap]
rs2305980	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs28405622	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28468660	0.92[ASN][1000 genomes]
rs4696597	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62346572	1.00[ASN][1000 genomes]
rs9884665	1.00[JPT][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12374344	TIGD4	cis	parietal	SCAN
rs12374344	C14orf39	trans	parietal	SCAN
rs12374344	CSTF2	trans	parietal	SCAN
rs12374344	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151097600-151129000	Weak transcription	Lung	lung
2	chr4:151098200-151128000	Weak transcription	Fetal Stomach	stomach
3	chr4:151100000-151127800	Weak transcription	Osteobl	bone
4	chr4:151101600-151127600	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:151103200-151138000	Weak transcription	NH-A	brain
6	chr4:151104200-151127400	Weak transcription	Fetal Brain Female	brain
7	chr4:151108600-151130000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr4:151108800-151129000	Weak transcription	Brain Hippocampus Middle	brain
9	chr4:151112600-151128200	Weak transcription	Left Ventricle	heart
10	chr4:151114200-151154200	Weak transcription	Aorta	Aorta
11	chr4:151115400-151127200	Weak transcription	HSMMtube	muscle
12	chr4:151117800-151128200	Weak transcription	Ovary	ovary
13	chr4:151118000-151127200	Weak transcription	Brain Anterior Caudate	brain
14	chr4:151118200-151127000	Weak transcription	Brain Germinal Matrix	brain
15	chr4:151118400-151128200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr4:151120000-151132200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:151120400-151128200	Weak transcription	A549	lung
18	chr4:151120400-151129000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:151122200-151137800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:151123800-151136800	Weak transcription	Fetal Intestine Large	intestine
21	chr4:151124000-151132200	Weak transcription	Right Ventricle	heart
22	chr4:151125200-151127000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:151125400-151127200	Strong transcription	HSMM	muscle
24	chr4:151126000-151128000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:151126200-151130200	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr4:151126400-151127800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:151126400-151128600	Enhancers	Fetal Lung	lung
28	chr4:151126600-151127600	Weak transcription	Brain Angular Gyrus	brain

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