Variant report

Variant	rs6700989
Chromosome Location	chr1:152139309-152139310
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:152138759..152140598-chr1:152141934..152143751,2	MCF-7	breast:
2	chr1:152019311..152021605-chr1:152136763..152140691,3	MCF-7	breast:
3	chr1:152134137..152136314-chr1:152136574..152139467,2	MCF-7	breast:
4	chr1:152008104..152009692-chr1:152138016..152140338,2	MCF-7	breast:
5	chr1:152006771..152009920-chr1:152134117..152139740,5	MCF-7	breast:
6	chr1:152114301..152115100-chr1:152139208..152139905,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10788821	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1131471	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1131473	0.80[EUR][1000 genomes]
rs11588437	0.81[EUR][1000 genomes]
rs12033735	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1496036	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496041	0.81[EUR][1000 genomes]
rs2496253	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2935208	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2999563	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3001974	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3001978	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3122305	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4579760	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4845419	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845420	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs924087	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547853	chr1:152008671-152236760	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv872442	chr1:152054120-152187641	Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6700989	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs6700989	S100A10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152131400-152145800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:152134800-152142200	Enhancers	HMEC	breast
3	chr1:152135800-152139600	Weak transcription	Hela-S3	cervix
4	chr1:152136000-152139600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:152136000-152139800	Weak transcription	NH-A	brain
6	chr1:152136200-152139400	Weak transcription	NHDF-Ad	bronchial
7	chr1:152136200-152140000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:152136400-152139600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:152137800-152139600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:152137800-152142800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:152138000-152139800	Weak transcription	Fetal Intestine Large	intestine
12	chr1:152138200-152139600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:152138400-152139400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:152138400-152139400	Weak transcription	NHEK	skin
15	chr1:152138400-152139800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:152138400-152141400	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr1:152138600-152139600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:152138600-152140600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:152138800-152139400	Enhancers	Adipose Nuclei	Adipose
20	chr1:152138800-152140400	Weak transcription	GM12878-XiMat	blood
21	chr1:152138800-152141800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr1:152139000-152139400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:152139200-152141400	Enhancers	HSMMtube	muscle
24	chr1:152139200-152141600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:152139200-152141600	Enhancers	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links