Variant report

Variant	rs36528
Chromosome Location	chr14:71941135-71941136
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71931431..71933043-chr14:71940078..71941973,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10129301	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10130652	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10143346	0.87[ASN][1000 genomes]
rs10147863	0.82[YRI][hapmap]
rs11628525	0.90[CHB][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs12878009	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12897119	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12897977	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs193440	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2041330	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2108048	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3088206	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36532	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36535	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41217	0.85[ASN][1000 genomes]
rs41218	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs41219	0.81[EUR][1000 genomes]
rs41225	0.82[EUR][1000 genomes]
rs41229	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4464023	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4899396	0.85[EUR][1000 genomes]
rs6574014	0.81[ASN][1000 genomes]
rs7141155	0.80[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.91[YRI][hapmap]
rs7153726	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7154208	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8007271	0.81[EUR][1000 genomes]
rs8007521	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8016217	0.88[CEU][hapmap];0.84[CHB][hapmap];0.80[TSI][hapmap]
rs8023058	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs917391	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498021	chr14:71874708-72128721	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3398985	chr14:71927884-72404676	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs36528	VSX2	cis	parietal	SCAN
rs36528	SLC8A3	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71922200-71944600	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr14:71928000-71944800	Weak transcription	Primary B cells from cord blood	blood
3	chr14:71929200-71964200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr14:71930200-71954200	Weak transcription	Gastric	stomach
5	chr14:71930200-71955600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr14:71931200-71948800	Weak transcription	Aorta	Aorta
7	chr14:71934200-71941400	Weak transcription	Colon Smooth Muscle	Colon
8	chr14:71934400-71946400	Weak transcription	Adipose Nuclei	Adipose
9	chr14:71935400-71980400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr14:71936200-71942400	Weak transcription	Primary T cells from cord blood	blood
11	chr14:71936400-71951400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr14:71938400-71941200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr14:71938400-71941200	Enhancers	NHDF-Ad	bronchial
14	chr14:71938400-71943200	Enhancers	Osteobl	bone
15	chr14:71938400-71943600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr14:71938600-71941200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr14:71938600-71941400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr14:71939000-71942600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr14:71939000-71945400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr14:71939000-71945400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr14:71939000-71950400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr14:71939000-71959800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr14:71939200-71942000	Enhancers	Hela-S3	cervix
24	chr14:71939200-71955800	Weak transcription	NHLF	lung
25	chr14:71939400-71942400	Weak transcription	Dnd41	blood
26	chr14:71939400-71945600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr14:71939800-71942600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr14:71939800-71942600	Enhancers	GM12878-XiMat	blood
29	chr14:71939800-71944400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr14:71939800-71954200	Weak transcription	Small Intestine	intestine
31	chr14:71940200-71942200	Enhancers	Fetal Heart	heart
32	chr14:71940200-71942800	Enhancers	Brain Anterior Caudate	brain
33	chr14:71940200-71943000	Enhancers	Brain Germinal Matrix	brain
34	chr14:71940200-71943200	Enhancers	Brain Angular Gyrus	brain
35	chr14:71940200-71943200	Enhancers	Brain Hippocampus Middle	brain
36	chr14:71940400-71941200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr14:71940400-71941400	Enhancers	HMEC	breast
38	chr14:71940400-71941600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr14:71940400-71941600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr14:71940400-71943200	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr14:71940600-71941200	Enhancers	Spleen	Spleen
42	chr14:71940600-71941400	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr14:71940600-71941400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr14:71940600-71941600	Enhancers	Fetal Brain Female	brain
45	chr14:71940600-71941600	Enhancers	HSMMtube	muscle
46	chr14:71940600-71942000	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr14:71940600-71942000	Enhancers	Brain Substantia Nigra	brain
48	chr14:71940600-71943000	Enhancers	Brain Cingulate Gyrus	brain
49	chr14:71940600-71943000	Enhancers	Fetal Lung	lung
50	chr14:71940800-71941200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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