Variant report

Variant	rs12435904
Chromosome Location	chr14:65121102-65121103
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64968793..64973673-chr14:65119564..65122078,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126804	Chromatin interaction
ENSG00000089775	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10873174	0.91[CHB][hapmap]
rs11158554	0.95[ASN][1000 genomes]
rs11158555	0.95[ASN][1000 genomes]
rs11622168	0.91[CHB][hapmap]
rs11848238	0.93[ASN][1000 genomes]
rs12431555	0.95[ASN][1000 genomes]
rs12432551	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12436296	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12884911	0.91[CHB][hapmap]
rs12893758	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17113846	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1950302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1956419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1956420	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2016351	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3742604	0.91[CHB][hapmap]
rs4899141	0.80[ASN][1000 genomes]
rs4902293	0.91[CHB][hapmap]
rs4902303	0.84[ASN][1000 genomes]
rs4902307	0.83[MEX][hapmap]
rs6573560	0.91[CHB][hapmap]
rs7142258	0.80[ASN][1000 genomes]
rs7143298	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7143397	0.82[ASN][1000 genomes]
rs733127	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs911000	0.80[ASN][1000 genomes]
rs9944101	0.95[CHB][hapmap];0.95[JPT][hapmap]

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	nsv1049097	chr14:65027753-65202018	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1008915	chr14:65117194-65126733	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12435904	PLEKHG3	cis	multi-tissue	Pritchard
rs12435904	ZBTB25	cis	parietal	SCAN
rs12435904	ZBTB25	cis	cerebellum	SCAN
rs12435904	CEP70	trans	parietal	SCAN
rs12435904	SIX1	cis	cerebellum	SCAN
rs12435904	VTI1B	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65116800-65121200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr14:65116800-65121200	Weak transcription	Spleen	Spleen
3	chr14:65116800-65125000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:65117000-65128400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr14:65119200-65121200	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr14:65119400-65121200	Weak transcription	Psoas Muscle	Psoas
7	chr14:65120200-65122200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr14:65120400-65121200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr14:65120400-65121200	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr14:65120400-65121200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr14:65120400-65121200	Enhancers	NHDF-Ad	bronchial
12	chr14:65120400-65121800	Enhancers	HSMMtube	muscle
13	chr14:65120400-65122000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr14:65120400-65122000	Enhancers	HSMM	muscle
15	chr14:65120400-65122000	Enhancers	NHLF	lung
16	chr14:65120400-65122200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr14:65120400-65122200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr14:65120400-65122200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr14:65120400-65122200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr14:65120400-65122200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr14:65120400-65122200	Enhancers	Fetal Muscle Leg	muscle
22	chr14:65120400-65122600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr14:65120600-65121200	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr14:65120600-65121400	Enhancers	Placenta Amnion	Placenta Amnion
25	chr14:65120600-65121600	Enhancers	GM12878-XiMat	blood
26	chr14:65120600-65121600	Enhancers	NHEK	skin
27	chr14:65120600-65121800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr14:65120600-65121800	Enhancers	HMEC	breast
29	chr14:65120600-65121800	Enhancers	HUVEC	blood vessel
30	chr14:65120600-65122000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr14:65120600-65122000	Enhancers	Primary hematopoietic stem cells	blood
32	chr14:65120600-65122000	Enhancers	NH-A	brain
33	chr14:65120600-65122200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr14:65120600-65122200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr14:65120600-65122200	Enhancers	Adipose Nuclei	Adipose
36	chr14:65120600-65122200	Enhancers	Liver	Liver
37	chr14:65120600-65122200	Enhancers	Colon Smooth Muscle	Colon
38	chr14:65120600-65122200	Enhancers	Placenta	Placenta
39	chr14:65120600-65122200	Enhancers	Rectal Smooth Muscle	rectum
40	chr14:65120600-65122200	Enhancers	Right Ventricle	heart
41	chr14:65120800-65121200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr14:65120800-65121200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr14:65120800-65121200	Enhancers	Brain Cingulate Gyrus	brain
44	chr14:65120800-65121200	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr14:65120800-65121400	Enhancers	Small Intestine	intestine
46	chr14:65120800-65121400	Flanking Active TSS	A549	lung
47	chr14:65120800-65121600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr14:65120800-65121800	Weak transcription	Right Atrium	heart
49	chr14:65120800-65122200	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr14:65121000-65121200	Enhancers	Pancreas	Pancrea

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