Variant report

Variant	rs13435543
Chromosome Location	chr4:151040829-151040830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:151040500..151042275-chr4:151050939..151052686,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10027662	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10031412	0.81[EUR][1000 genomes]
rs28360726	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28392881	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28397206	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28439804	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28513621	0.81[EUR][1000 genomes]
rs28559901	0.81[EUR][1000 genomes]
rs28605560	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28642700	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28654919	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28665284	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28806288	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28887006	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28896206	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4259040	0.80[EUR][1000 genomes]
rs4339189	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56150320	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57168672	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61361070	0.81[EUR][1000 genomes]
rs62338190	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62339909	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6848344	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]
rs9784426	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9968348	0.81[EUR][1000 genomes]
rs9968351	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9985766	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9986068	1.00[CHB][hapmap]
rs9992748	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[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	nsv530158	chr4:150877557-151040992	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	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
5	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13435543	DCLK2	cis	Whole Blood	GTEx
rs13435543	LRBA	cis	cerebellum	SCAN
rs13435543	LRBA	Cis_1M	lymphoblastoid	RTeQTL
rs13435543	TIGD4	cis	parietal	SCAN
rs13435543	DCHS2	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151036200-151042600	Weak transcription	Brain Substantia Nigra	brain
2	chr4:151036400-151042400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:151037400-151048400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:151038200-151051600	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:151038400-151043800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:151038800-151070000	Weak transcription	Ovary	ovary
7	chr4:151039000-151042600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:151039000-151048000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr4:151039000-151048600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:151039000-151052800	Weak transcription	Right Ventricle	heart
11	chr4:151039400-151042800	Weak transcription	Brain Anterior Caudate	brain
12	chr4:151039400-151044800	Weak transcription	Aorta	Aorta
13	chr4:151039400-151047200	Weak transcription	NHLF	lung
14	chr4:151040000-151041800	Enhancers	Osteobl	bone
15	chr4:151040000-151042600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:151040200-151041200	Enhancers	HepG2	liver
17	chr4:151040200-151041400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr4:151040200-151041800	Enhancers	HUVEC	blood vessel
19	chr4:151040400-151041200	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr4:151040400-151041200	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr4:151040400-151041400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr4:151040400-151041600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr4:151040400-151041600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:151040400-151041600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:151040400-151041600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:151040400-151041600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:151040400-151041600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:151040400-151041600	Enhancers	NH-A	brain
29	chr4:151040400-151041800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr4:151040400-151041800	Enhancers	HSMMtube	muscle
31	chr4:151040400-151041800	Enhancers	NHDF-Ad	bronchial
32	chr4:151040400-151042000	Enhancers	HSMM	muscle
33	chr4:151040600-151041000	Enhancers	Fetal Heart	heart
34	chr4:151040600-151041200	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr4:151040600-151041200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:151040600-151041200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:151040600-151041200	Enhancers	NHEK	skin
38	chr4:151040600-151041400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr4:151040600-151041600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr4:151040600-151041600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:151040600-151041800	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr4:151040800-151041000	Enhancers	Muscle Satellite Cultured Cells	--
43	chr4:151040800-151041200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr4:151040800-151041200	Active TSS	A549	lung
45	chr4:151040800-151042600	Weak transcription	Colon Smooth Muscle	Colon

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