Variant report

Variant	rs6848344
Chromosome Location	chr4:151049132-151049133
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10003178	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10004630	0.83[AFR][1000 genomes]
rs10011368	0.83[AFR][1000 genomes]
rs10014266	0.83[AFR][1000 genomes]
rs10018922	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10022936	0.83[AFR][1000 genomes]
rs10026506	0.83[AFR][1000 genomes]
rs10027662	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10031412	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13435543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28360726	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs28374205	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs28392881	0.87[ASN][1000 genomes]
rs28397206	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs28413051	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs28416593	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs28423983	0.83[AFR][1000 genomes]
rs28439804	0.87[ASN][1000 genomes]
rs28501175	0.85[AFR][1000 genomes]
rs28513621	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs28559901	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs28605560	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28642700	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28654919	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs28665284	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28714207	0.81[ASN][1000 genomes]
rs28735454	0.83[AFR][1000 genomes]
rs28806288	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28887006	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs28896206	0.87[ASN][1000 genomes]
rs4259040	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4339189	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4356899	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4423856	0.83[AFR][1000 genomes]
rs4631016	0.83[AFR][1000 genomes]
rs56150320	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57168672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60160057	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs61361070	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs62338190	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62339860	0.83[AFR][1000 genomes]
rs62339861	0.83[AFR][1000 genomes]
rs62339874	0.83[AFR][1000 genomes]
rs62339875	0.83[AFR][1000 genomes]
rs62339876	0.83[AFR][1000 genomes]
rs62339877	0.83[AFR][1000 genomes]
rs62339878	0.83[AFR][1000 genomes]
rs62339880	0.83[AFR][1000 genomes]
rs62339909	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7659009	0.83[AFR][1000 genomes]
rs9307863	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9784426	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9968348	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9968351	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9985766	1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9986068	1.00[CHB][hapmap]
rs9992748	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[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	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	esv3367011	chr4:151049031-151053489	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
6	esv3467428	chr4:151049063-151053482	Enhancers Weak transcription Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
7	esv3467429	chr4:151049063-151053482	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6848344	LRBA	Cis_1M	lymphoblastoid	RTeQTL
rs6848344	DCLK2	cis	Whole Blood	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151038200-151051600	Weak transcription	Brain Hippocampus Middle	brain
2	chr4:151038800-151070000	Weak transcription	Ovary	ovary
3	chr4:151039000-151052800	Weak transcription	Right Ventricle	heart
4	chr4:151043200-151052200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:151043400-151051600	Weak transcription	Brain Substantia Nigra	brain
6	chr4:151044200-151052800	Weak transcription	Brain Germinal Matrix	brain
7	chr4:151044600-151049400	Enhancers	Primary B cells from peripheral blood	blood
8	chr4:151045200-151099000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:151045400-151052800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr4:151047200-151049600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:151047200-151049600	Enhancers	NHDF-Ad	bronchial
12	chr4:151047200-151049800	Enhancers	NHLF	lung
13	chr4:151047200-151050000	Enhancers	HSMMtube	muscle
14	chr4:151047200-151050200	Enhancers	HSMM	muscle
15	chr4:151047200-151050400	Enhancers	Osteobl	bone
16	chr4:151047400-151049200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:151047400-151049200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:151047400-151049400	Enhancers	NHEK	skin
19	chr4:151047400-151058200	Weak transcription	Left Ventricle	heart
20	chr4:151047600-151049200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:151047800-151049200	Enhancers	HMEC	breast
22	chr4:151047800-151051600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:151048000-151049200	Enhancers	Brain Cingulate Gyrus	brain
24	chr4:151048000-151050400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:151048200-151049400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:151048200-151049600	Weak transcription	Fetal Heart	heart
27	chr4:151048200-151050400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr4:151048200-151050400	Enhancers	NH-A	brain
29	chr4:151048200-151050600	Enhancers	A549	lung
30	chr4:151048200-151051800	Weak transcription	Colon Smooth Muscle	Colon
31	chr4:151048400-151049200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:151048400-151049200	Enhancers	Primary B cells from cord blood	blood
33	chr4:151048400-151051800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:151048400-151057000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:151048600-151049600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:151048600-151049600	Enhancers	Brain Anterior Caudate	brain
37	chr4:151048800-151049200	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr4:151048800-151049600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:151049000-151049400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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