Variant report

Variant	rs2973456
Chromosome Location	chr5:90395882-90395883
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90217916..90220914-chr5:90395407..90397788,2	MCF-7	breast:
2	chr5:90394429..90396427-chr5:90677263..90679186,2	K562	blood:
3	chr5:90395373..90399568-chr5:90677552..90681506,8	MCF-7	breast:
4	chr5:90389673..90399904-chr5:90673387..90683638,16	K562	blood:
5	chr5:90395712..90398917-chr5:90520735..90523244,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251093	Chromatin interaction
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12109264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16869403	0.81[CEU][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs16869404	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16869414	0.90[CEU][hapmap]
rs16869425	1.00[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1852731	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886924	0.80[CEU][hapmap]
rs2950849	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2950850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.98[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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950853	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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];0.95[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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973444	0.90[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];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];0.95[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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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];0.98[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3952745	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]
rs56137437	0.81[EUR][1000 genomes]
rs56377639	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58524182	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59654682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59661306	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66482530	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs66608099	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6874106	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs73189007	1.00[ASN][1000 genomes]
rs73189008	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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
rs2973456	TMEM14C	trans	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90370600-90397600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:90385800-90397400	Weak transcription	Fetal Lung	lung
3	chr5:90386800-90400800	Weak transcription	K562	blood
4	chr5:90387800-90397600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:90391000-90397000	Weak transcription	A549	lung
6	chr5:90391800-90397600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr5:90392000-90397400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:90392000-90397400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:90392000-90400800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:90392200-90400800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:90392600-90399200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr5:90392600-90400800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:90392800-90397400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:90392800-90397400	Weak transcription	Brain Anterior Caudate	brain
15	chr5:90392800-90400800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:90393000-90397400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:90393000-90397400	Weak transcription	Fetal Brain Male	brain
18	chr5:90393000-90397600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:90393200-90397400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:90393600-90402600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:90394400-90397400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:90394400-90397400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr5:90394400-90398200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr5:90394400-90402800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:90394600-90397600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr5:90394600-90397600	Weak transcription	Fetal Kidney	kidney
27	chr5:90394600-90397600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr5:90394800-90397400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr5:90394800-90397400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:90394800-90397400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:90395000-90397600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr5:90395200-90397400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr5:90395200-90397400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:90395200-90397800	Weak transcription	Colon Smooth Muscle	Colon
35	chr5:90395200-90399400	Weak transcription	NHDF-Ad	bronchial
36	chr5:90395400-90397400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:90395400-90406000	Weak transcription	Fetal Heart	heart
38	chr5:90395400-90415200	Weak transcription	Left Ventricle	heart
39	chr5:90395600-90396000	Weak transcription	Esophagus	oesophagus
40	chr5:90395600-90400400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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