Variant report

Variant	rs3952745
Chromosome Location	chr5:90405835-90405836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90405182..90407708-chr5:90411248..90414003,2	MCF-7	breast:
2	chr5:90398100..90399862-chr5:90403855..90405931,2	K562	blood:
3	chr5:90403057..90405886-chr5:90674744..90678656,3	MCF-7	breast:
4	chr5:90405497..90409184-chr5:90675252..90678679,4	K562	blood:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12109264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16869403	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs16869404	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16869414	0.90[CEU][hapmap]
rs16869425	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1852731	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1876635	0.81[CEU][hapmap]
rs1986718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886924	0.80[CEU][hapmap]
rs2950849	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2950850	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950852	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950853	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2950855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973444	0.90[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs2973445	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973455	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112484	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56377639	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58524182	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59654682	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59661306	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66482530	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66608099	0.81[AMR][1000 genomes]
rs6874106	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs73189007	1.00[ASN][1000 genomes]
rs73189008	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3952745	TMEM14C	trans	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90395400-90406000	Weak transcription	Fetal Heart	heart
2	chr5:90395400-90415200	Weak transcription	Left Ventricle	heart
3	chr5:90396200-90422800	Weak transcription	Esophagus	oesophagus
4	chr5:90398200-90406200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:90398200-90406400	Weak transcription	Brain Angular Gyrus	brain
6	chr5:90399400-90406200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:90401400-90406200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:90401600-90431800	Weak transcription	K562	blood
9	chr5:90402200-90407200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:90402400-90413600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:90403000-90415600	Weak transcription	Right Atrium	heart
12	chr5:90403000-90431600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:90403200-90406600	Weak transcription	Psoas Muscle	Psoas
14	chr5:90403200-90431600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:90403400-90418800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:90403400-90418800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:90405200-90407600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:90405200-90408200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:90405200-90408200	Enhancers	Brain Anterior Caudate	brain
20	chr5:90405200-90408200	Enhancers	NHDF-Ad	bronchial
21	chr5:90405400-90406800	Enhancers	Fetal Muscle Leg	muscle
22	chr5:90405400-90407000	Enhancers	Brain Hippocampus Middle	brain
23	chr5:90405400-90407800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:90405400-90408200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr5:90405400-90409000	Enhancers	Fetal Brain Male	brain
26	chr5:90405600-90406400	Weak transcription	NHLF	lung
27	chr5:90405600-90406600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:90405800-90406800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:90405800-90410800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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