Variant report

Variant	rs6874106
Chromosome Location	chr5:90371776-90371777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:90370618..90372273-chr5:90676246..90679128,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12109264	0.88[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs16869403	0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16869404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869414	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16869425	0.90[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1852731	0.90[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1876635	0.90[CEU][hapmap];0.91[CHB][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap]
rs1986718	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs2950849	0.90[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2950850	0.82[AMR][1000 genomes]
rs2950851	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs2950852	0.81[CEU][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs2950853	0.82[AMR][1000 genomes]
rs2950854	0.90[CEU][hapmap]
rs2950855	0.90[CEU][hapmap]
rs2973445	0.90[CEU][hapmap]
rs2973447	0.90[CEU][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes]
rs2973448	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs2973449	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs2973450	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs2973453	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs2973454	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs2973455	0.82[AMR][1000 genomes]
rs2973456	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs3112484	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs3952745	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs56137437	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56377639	0.82[AMR][1000 genomes]
rs58524182	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59654682	0.82[AMR][1000 genomes]
rs59661306	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61392689	0.93[ASN][1000 genomes]
rs66482530	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66608099	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73187190	0.93[ASN][1000 genomes]
rs73189008	0.82[AMR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6874106	MCTP1	cis	cerebellum	SCAN
rs6874106	TMEM14C	trans	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90341200-90376600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr5:90358400-90391000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:90358600-90375400	Weak transcription	Brain Anterior Caudate	brain
4	chr5:90360200-90386400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:90366600-90386600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:90367000-90378000	Weak transcription	Fetal Brain Female	brain
7	chr5:90367200-90377600	Weak transcription	K562	blood
8	chr5:90368200-90372600	Enhancers	Osteobl	bone
9	chr5:90368400-90372200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:90368400-90372400	Enhancers	NHDF-Ad	bronchial
11	chr5:90368400-90372600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:90368400-90374400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:90369000-90373000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:90369000-90374400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:90369400-90373000	Weak transcription	NHEK	skin
16	chr5:90369400-90374400	Weak transcription	Aorta	Aorta
17	chr5:90369400-90374400	Weak transcription	Colon Smooth Muscle	Colon
18	chr5:90369400-90374400	Weak transcription	Fetal Kidney	kidney
19	chr5:90369400-90374600	Weak transcription	Hela-S3	cervix
20	chr5:90369400-90386200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:90369600-90373000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:90369600-90373000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:90369600-90373400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:90369600-90386000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr5:90370200-90374200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:90370400-90372600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:90370600-90373000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:90370600-90397600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:90370800-90371800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr5:90370800-90372400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:90371000-90372600	Weak transcription	A549	lung
32	chr5:90371200-90372000	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links