Variant report

Variant	rs28361896
Chromosome Location	chr4:151066655-151066656
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:151065674..151068783-chr4:151069402..151072348,3	MCF-7	breast:
2	chr4:151064651..151066657-chr4:151066791..151068654,2	MCF-7	breast:
3	chr4:151066204..151068081-chr4:151071216..151073291,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10001645	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10001651	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10020361	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10029811	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10033999	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10520059	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12019295	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17026748	0.88[AMR][1000 genomes]
rs28377256	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28501175	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28598870	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28605560	0.83[EUR][1000 genomes]
rs28616626	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28635652	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28673979	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4353883	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59085186	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60526300	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62338190	0.80[EUR][1000 genomes]
rs62338194	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62338212	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62338216	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72732403	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7438777	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9884239	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9884665	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9997755	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28361896	DCLK2	cis	Whole Blood	GTEx
rs28361896	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151038800-151070000	Weak transcription	Ovary	ovary
2	chr4:151045200-151099000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:151049200-151074000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr4:151057800-151070600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:151061800-151069800	Weak transcription	Left Ventricle	heart
6	chr4:151061800-151071800	Weak transcription	Brain Anterior Caudate	brain
7	chr4:151062800-151066800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:151062800-151067000	Weak transcription	HMEC	breast
9	chr4:151062800-151071800	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:151062800-151072000	Weak transcription	Aorta	Aorta
11	chr4:151063000-151070800	Weak transcription	HSMMtube	muscle
12	chr4:151063200-151067200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:151063200-151070600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:151063400-151070600	Weak transcription	Fetal Heart	heart
15	chr4:151063600-151066800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:151063600-151070200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:151064400-151066800	Weak transcription	Fetal Lung	lung
18	chr4:151064600-151080200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:151065800-151067400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:151066000-151067800	Enhancers	Osteobl	bone
21	chr4:151066400-151067400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr4:151066400-151067400	Enhancers	NHLF	lung
23	chr4:151066400-151067600	Enhancers	Hela-S3	cervix
24	chr4:151066400-151067600	Enhancers	NH-A	brain
25	chr4:151066400-151067600	Enhancers	NHDF-Ad	bronchial
26	chr4:151066400-151067800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:151066400-151068000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr4:151066400-151068200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:151066400-151071800	Weak transcription	Fetal Stomach	stomach
30	chr4:151066600-151066800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:151066600-151066800	Flanking Active TSS	A549	lung
32	chr4:151066600-151067600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:151066600-151067800	Enhancers	HSMM	muscle
34	chr4:151066600-151067800	Enhancers	NHEK	skin

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