Variant report

Variant	rs4075104
Chromosome Location	chr14:106000214-106000215
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:105993630..105997009-chr14:105997859..106001918,6	K562	blood:
2	chr14:105955131..105957877-chr14:105998324..106001046,2	MCF-7	breast:
3	chr14:105995043..105996961-chr14:105997844..106000357,2	MCF-7	breast:
4	chr14:105997452..106000528-chr14:106001477..106004832,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM121-1	chr14:105999306-106000652	NONHSAT040375

Variant related genes	Relation type
ENSG00000230157	Chromatin interaction
ENSG00000184986	Chromatin interaction
ENSG00000185347	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10133083	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10136015	0.86[EUR][1000 genomes]
rs10139300	0.85[EUR][1000 genomes]
rs10139744	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10142224	0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs10143553	0.89[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs10147392	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10151805	0.85[EUR][1000 genomes]
rs10152050	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11624007	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11628497	0.85[EUR][1000 genomes]
rs12717698	0.85[EUR][1000 genomes]
rs12893999	0.85[EUR][1000 genomes]
rs13379293	0.86[EUR][1000 genomes]
rs28402171	0.86[EUR][1000 genomes]
rs28431397	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28529526	0.91[ASN][1000 genomes]
rs28662250	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28733392	0.99[EUR][1000 genomes]
rs35240373	0.80[EUR][1000 genomes]
rs35471125	0.80[EUR][1000 genomes]
rs35590487	1.00[CEU][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs35592422	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35723046	0.81[EUR][1000 genomes]
rs35921705	0.80[EUR][1000 genomes]
rs4074453	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];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074937	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4075105	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55958808	0.86[EUR][1000 genomes]
rs58087925	0.86[EUR][1000 genomes]
rs6576111	0.91[ASN][1000 genomes]
rs66710832	0.81[EUR][1000 genomes]
rs7141834	0.85[EUR][1000 genomes]
rs7160093	0.86[ASN][1000 genomes]
rs7160747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72713323	0.80[EUR][1000 genomes]
rs73373734	0.91[ASN][1000 genomes]
rs7493501	0.88[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs8003942	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs8004007	0.85[EUR][1000 genomes]
rs8005568	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs8013055	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs8013827	0.95[CEU][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs8014713	0.86[EUR][1000 genomes]
rs8014913	0.86[EUR][1000 genomes]
rs8021330	0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530813	chr14:105607701-106453697	Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4075104	TMEM121	cis	multi-tissue	Pritchard
rs4075104	TMEM121	cis	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:105994800-106001400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:105995400-106004200	Weak transcription	Brain Substantia Nigra	brain
3	chr14:105996000-106004000	Weak transcription	Pancreas	Pancrea
4	chr14:105996200-106004400	Weak transcription	Right Atrium	heart
5	chr14:105996600-106004400	Weak transcription	Liver	Liver
6	chr14:105996800-106004000	Weak transcription	Fetal Brain Male	brain
7	chr14:105997400-106000600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr14:105997400-106001000	Weak transcription	Brain Hippocampus Middle	brain
9	chr14:105997400-106001600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr14:105997400-106004200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr14:105997600-106000400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr14:105998200-106004400	Weak transcription	Brain Germinal Matrix	brain
13	chr14:105999200-106001000	Weak transcription	Fetal Brain Female	brain
14	chr14:105999600-106004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr14:105999800-106003200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr14:106000200-106000400	Enhancers	Fetal Lung	lung
17	chr14:106000200-106004000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr14:106000200-106004000	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links