Variant report

Variant	rs12957388
Chromosome Location	chr18:7953419-7953420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:7953033..7955520-chr18:7955662..7957889,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10153443	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12326176	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs12326185	0.86[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12954431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956961	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs12957993	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs12959314	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12960276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12963759	0.91[EUR][1000 genomes]
rs12966777	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12968232	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13381485	0.86[EUR][1000 genomes]
rs16952586	1.00[CHB][hapmap]
rs16952705	1.00[ASW][hapmap];0.93[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16952722	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];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28434244	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34017251	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34046553	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34049036	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34296167	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34554615	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34580701	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35308699	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35434291	0.83[EUR][1000 genomes]
rs35521625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35558945	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35822807	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35830277	0.87[EUR][1000 genomes]
rs36093720	0.86[EUR][1000 genomes]
rs7239786	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs7240582	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs8087770	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs8087884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8089133	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8092781	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9807495	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9952741	0.80[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9956981	0.86[EUR][1000 genomes]
rs9961079	0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9966320	1.00[CHB][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	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12957388	NAPG	cis	parietal	SCAN
rs12957388	BOK	trans	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7932200-7961000	Weak transcription	HepG2	liver
2	chr18:7937600-7955200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr18:7941400-7955000	Weak transcription	Psoas Muscle	Psoas
4	chr18:7941800-7966400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr18:7942000-7955200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr18:7942000-7955200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr18:7942200-7955200	Weak transcription	Fetal Muscle Leg	muscle
8	chr18:7946200-7958200	Weak transcription	Aorta	Aorta
9	chr18:7946800-7955000	Weak transcription	Fetal Lung	lung
10	chr18:7947000-7954200	Weak transcription	Fetal Kidney	kidney
11	chr18:7947200-7955600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr18:7947200-7955800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr18:7947200-7958200	Weak transcription	Colon Smooth Muscle	Colon
14	chr18:7947200-7981400	Weak transcription	Fetal Stomach	stomach
15	chr18:7947400-7955400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr18:7947400-7958200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr18:7947400-7958400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr18:7947400-7959200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr18:7947400-7963400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr18:7947400-7963600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr18:7947400-7965600	Weak transcription	Thymus	Thymus
22	chr18:7947600-7955400	Weak transcription	Brain Angular Gyrus	brain
23	chr18:7947600-7956600	Weak transcription	Brain Hippocampus Middle	brain
24	chr18:7947600-7958200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr18:7947800-7954000	Weak transcription	NHLF	lung
26	chr18:7947800-7955200	Weak transcription	Right Atrium	heart
27	chr18:7947800-7955200	Weak transcription	Right Ventricle	heart
28	chr18:7947800-7957000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr18:7947800-7957400	Weak transcription	Spleen	Spleen
30	chr18:7947800-7958400	Weak transcription	Brain Anterior Caudate	brain
31	chr18:7947800-7958400	Weak transcription	Gastric	stomach
32	chr18:7947800-7958600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr18:7947800-7967600	Weak transcription	Primary T cells from cord blood	blood
34	chr18:7948000-7953600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr18:7948000-7955200	Weak transcription	Ovary	ovary
36	chr18:7948000-7955400	Weak transcription	Fetal Thymus	thymus
37	chr18:7948000-7956600	Weak transcription	Lung	lung
38	chr18:7948000-7957000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr18:7948000-7959600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr18:7948000-7965800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr18:7948000-7967200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr18:7948000-7975000	Weak transcription	Pancreas	Pancrea
43	chr18:7950800-7956200	Weak transcription	Fetal Intestine Small	intestine
44	chr18:7951000-7958600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr18:7951200-7953800	Weak transcription	NHDF-Ad	bronchial
46	chr18:7951200-7954000	Weak transcription	HUVEC	blood vessel
47	chr18:7951200-7955000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr18:7951200-7955200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr18:7951200-7958000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr18:7951200-7958200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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