Variant report

Variant	rs8009733
Chromosome Location	chr14:77740127-77740128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:77738903..77740778-chr14:77763967..77766805,2	MCF-7	breast:
2	chr14:77597295..77599304-chr14:77739506..77741172,2	MCF-7	breast:
3	chr14:77736936..77738767-chr14:77739466..77741351,2	MCF-7	breast:
4	chr14:77738568..77742274-chr14:77786037..77788783,3	MCF-7	breast:
5	chr14:77735572..77739063-chr14:77740094..77742423,3	K562	blood:

Variant related genes	Relation type
ENSG00000009830	Chromatin interaction
ENSG00000165553	Chromatin interaction
ENSG00000100577	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10138030	0.95[CHD][hapmap];0.83[JPT][hapmap]
rs1055592	0.89[CHD][hapmap]
rs11159254	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11547793	0.98[CHD][hapmap];0.87[JPT][hapmap]
rs11547794	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624564	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11627257	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs1600005	0.89[ASN][1000 genomes]
rs17105672	0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs2042045	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs2111699	0.82[CHB][hapmap]
rs2193594	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2216089	0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2270421	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2287387	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs2287388	0.95[CHD][hapmap];0.87[JPT][hapmap]
rs2287392	0.95[CHD][hapmap];0.87[JPT][hapmap]
rs2363641	0.86[CHB][hapmap]
rs2363643	0.82[CHB][hapmap]
rs3783986	0.91[CHD][hapmap];0.95[JPT][hapmap]
rs3783988	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs3783989	0.87[JPT][hapmap]
rs3815626	0.86[CHB][hapmap]
rs4147578	0.82[CHB][hapmap]
rs4899650	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4903565	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4903567	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs59730492	0.83[ASN][1000 genomes]
rs61990261	0.85[ASN][1000 genomes]
rs6574367	0.86[CHB][hapmap]
rs7142812	0.86[CHB][hapmap]
rs7158951	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7159558	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8009261	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431017	chr14:76938089-77854647	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv1361	chr14:77707417-77753024	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv902104	chr14:77720741-77756321	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8009733	NRXN3	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77737400-77743000	Weak transcription	Dnd41	blood
2	chr14:77737800-77742800	Weak transcription	Gastric	stomach
3	chr14:77738000-77742600	Weak transcription	Pancreas	Pancrea
4	chr14:77738000-77742600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr14:77738200-77742400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr14:77738800-77741800	Weak transcription	Brain Germinal Matrix	brain
7	chr14:77738800-77743400	Weak transcription	A549	lung
8	chr14:77738800-77749600	Weak transcription	NHDF-Ad	bronchial
9	chr14:77739000-77749800	Weak transcription	HUVEC	blood vessel
10	chr14:77739200-77740200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr14:77739200-77742000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr14:77739200-77742400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr14:77739200-77742600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr14:77739200-77742600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr14:77739200-77742600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr14:77739200-77742600	Weak transcription	Fetal Intestine Large	intestine
17	chr14:77739200-77743600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr14:77739400-77741800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr14:77739400-77742600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr14:77739400-77742800	Weak transcription	Primary T cells from cord blood	blood
21	chr14:77739400-77744600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr14:77739400-77745400	Weak transcription	Fetal Lung	lung
23	chr14:77739400-77749000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr14:77739600-77740800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr14:77739600-77741400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr14:77739600-77741400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr14:77739600-77742000	Weak transcription	Esophagus	oesophagus
28	chr14:77739600-77742000	Weak transcription	Placenta	Placenta
29	chr14:77739600-77742400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr14:77739600-77742800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr14:77739600-77744400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr14:77739600-77745400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr14:77739600-77745600	Weak transcription	Primary B cells from cord blood	blood
34	chr14:77739600-77775600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr14:77739800-77741000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
36	chr14:77739800-77741600	Weak transcription	Fetal Brain Female	brain
37	chr14:77739800-77742200	Weak transcription	Brain Anterior Caudate	brain
38	chr14:77739800-77742200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr14:77739800-77743400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr14:77739800-77743400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr14:77739800-77743800	Weak transcription	HSMMtube	muscle
42	chr14:77740000-77740200	ZNF genes & repeats	Brain Hippocampus Middle	brain
43	chr14:77740000-77742400	Weak transcription	Right Ventricle	heart
44	chr14:77740000-77742600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr14:77740000-77744600	Weak transcription	Colonic Mucosa	Colon
46	chr14:77740000-77744600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr14:77740000-77749600	Weak transcription	HMEC	breast

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