Variant report

Variant	rs12514686
Chromosome Location	chr5:96071536-96071537
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	GATA3	chr5:96070654-96071571	SK-N-SH	brain:	n/a	chr5:96071164-96071174 chr5:96071076-96071087

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:96070439..96072973-chr5:96078050..96080855,3	K562	blood:
2	chr5:95996969..95998528-chr5:96069888..96071858,2	MCF-7	breast:

Variant related genes	Relation type
CAST	TF binding region
ENSG00000153113	Chromatin interaction
ENSG00000249180	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1037683	0.92[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12518441	0.92[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17086521	0.92[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17086550	0.92[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17086596	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086611	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086651	0.88[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes]
rs3816555	0.87[AMR][1000 genomes]
rs6862241	0.92[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7702304	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7718593	0.92[CHB][hapmap];0.88[GIH][hapmap];0.81[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	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv830411	chr5:96045168-96187817	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv516293	chr5:96070205-96216387	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12514686	LRAP	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96042800-96076200	Weak transcription	GM12878-XiMat	blood
2	chr5:96051000-96073600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:96051200-96076800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:96054800-96077200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:96057800-96075200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:96057800-96076000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr5:96057800-96098600	Weak transcription	Fetal Brain Male	brain
8	chr5:96058000-96077200	Weak transcription	Small Intestine	intestine
9	chr5:96058000-96078200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:96062800-96081400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:96063000-96126200	Weak transcription	Brain Germinal Matrix	brain
12	chr5:96064600-96092600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:96065400-96073200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:96065800-96073600	Weak transcription	HepG2	liver
15	chr5:96066400-96072600	Weak transcription	Pancreas	Pancrea
16	chr5:96066400-96073200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:96066400-96074400	Weak transcription	Colonic Mucosa	Colon
18	chr5:96066600-96072200	Weak transcription	HUVEC	blood vessel
19	chr5:96066600-96073200	Weak transcription	Brain Hippocampus Middle	brain
20	chr5:96066600-96073200	Weak transcription	HSMMtube	muscle
21	chr5:96066600-96073600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:96066600-96073800	Weak transcription	Fetal Stomach	stomach
23	chr5:96066600-96076000	Weak transcription	Aorta	Aorta
24	chr5:96066600-96076000	Weak transcription	Gastric	stomach
25	chr5:96066600-96076000	Weak transcription	Spleen	Spleen
26	chr5:96066600-96076800	Weak transcription	Fetal Thymus	thymus
27	chr5:96066800-96071800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr5:96066800-96072800	Weak transcription	Brain Anterior Caudate	brain
29	chr5:96066800-96073600	Weak transcription	Brain Angular Gyrus	brain
30	chr5:96066800-96077200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr5:96066800-96079400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr5:96067000-96071800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:96067000-96072000	Weak transcription	Adipose Nuclei	Adipose
34	chr5:96067000-96072000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:96067000-96072800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr5:96067000-96073000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr5:96067000-96073200	Weak transcription	Fetal Kidney	kidney
38	chr5:96067000-96073400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:96067000-96073400	Weak transcription	Ovary	ovary
40	chr5:96067000-96073600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr5:96067000-96073600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr5:96067000-96073800	Weak transcription	Brain Substantia Nigra	brain
43	chr5:96067200-96072400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr5:96067200-96072800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:96067200-96072800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr5:96067200-96073600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:96067200-96074200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr5:96067200-96076600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:96068200-96077200	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr5:96068200-96095400	Strong transcription	Primary T cells fromperipheralblood	blood

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