Variant report

Variant	rs3112484
Chromosome Location	chr5:90401221-90401222
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90398592..90401389-chr5:90514877..90517516,2	MCF-7	breast:
2	chr5:90399443..90402350-chr5:90413379..90415651,2	MCF-7	breast:
3	chr5:90396862..90402705-chr5:90677587..90681217,8	K562	blood:
4	chr5:90396522..90401651-chr5:90675518..90681239,15	MCF-7	breast:

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];0.94[YRI][hapmap];0.97[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];0.94[YRI][hapmap];0.80[AFR][1000 genomes];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];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950851	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950852	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950853	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950854	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2950855	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[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];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2973445	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973447	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973448	1.00[CEU][hapmap];0.86[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]
rs2973449	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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973450	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973453	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973454	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973455	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973456	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3952745	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	1.00[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	0.99[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	0.97[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
rs3112484	TMEM14C	trans	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90393600-90402600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:90394400-90402800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:90395400-90406000	Weak transcription	Fetal Heart	heart
4	chr5:90395400-90415200	Weak transcription	Left Ventricle	heart
5	chr5:90396200-90422800	Weak transcription	Esophagus	oesophagus
6	chr5:90398000-90402800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:90398200-90401400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:90398200-90402600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:90398200-90402600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:90398200-90405200	Weak transcription	Brain Anterior Caudate	brain
11	chr5:90398200-90406200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:90398200-90406400	Weak transcription	Brain Angular Gyrus	brain
13	chr5:90398400-90401600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:90399400-90406200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr5:90400200-90402400	Weak transcription	NHDF-Ad	bronchial
16	chr5:90400400-90401400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:90400800-90401400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:90400800-90401400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:90400800-90401600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:90400800-90401600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
21	chr5:90400800-90401600	Strong transcription	K562	blood
22	chr5:90400800-90402000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr5:90400800-90402200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:90401000-90401600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr5:90401000-90402200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
26	chr5:90401000-90402400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:90401200-90401600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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