Variant report

Variant	rs12145713
Chromosome Location	chr1:113739935-113739936
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113736472..113740505-chr1:113740581..113744406,4	MCF-7	breast:
2	chr1:113736589..113741335-chr1:113931781..113934442,4	MCF-7	breast:
3	chr1:113733744..113735445-chr1:113739417..113740943,2	MCF-7	breast:
4	chr1:113733582..113735336-chr1:113738656..113740345,2	K562	blood:
5	chr1:113738414..113740068-chr1:113740785..113743082,3	K562	blood:
6	chr1:113737370..113741159-chr1:113741484..113744250,4	K562	blood:
7	chr1:113737275..113741073-chr1:113748571..113751265,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC16A1-6	chr1:113739404-113741312	NONHSAT005321

No data

Variant related genes	Relation type
ENSG00000081026	Chromatin interaction
ENSG00000236887	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11102586	0.83[EUR][1000 genomes]
rs11102588	1.00[CEU][hapmap]
rs12117273	0.83[EUR][1000 genomes]
rs12118061	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118532	0.83[EUR][1000 genomes]
rs12118642	1.00[ASN][1000 genomes]
rs12119387	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120401	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120441	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120738	0.83[EUR][1000 genomes]
rs12123072	0.83[EUR][1000 genomes]
rs12123519	0.83[EUR][1000 genomes]
rs12123601	1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs12124148	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12125675	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125708	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126304	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127415	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128658	0.83[EUR][1000 genomes]
rs12129858	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133057	0.83[EUR][1000 genomes]
rs12136395	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137299	0.83[EUR][1000 genomes]
rs12139726	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139899	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140651	1.00[ASN][1000 genomes]
rs12140676	1.00[ASN][1000 genomes]
rs12140810	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141415	0.83[EUR][1000 genomes]
rs12141540	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141541	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142449	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142475	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142510	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143171	0.83[EUR][1000 genomes]
rs12143341	0.83[EUR][1000 genomes]
rs12143430	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145738	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]
rs1216767	0.83[EUR][1000 genomes]
rs1216793	1.00[TSI][hapmap]
rs1216808	1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs12184272	0.83[EUR][1000 genomes]
rs12184320	0.83[EUR][1000 genomes]
rs12744661	0.83[EUR][1000 genomes]
rs1310142	0.83[EUR][1000 genomes]
rs1618794	0.83[EUR][1000 genomes]
rs17031006	0.83[EUR][1000 genomes]
rs1728229	1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs1766864	1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs4839292	1.00[TSI][hapmap]
rs6695183	0.83[EUR][1000 genomes]
rs72685641	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7518115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541246	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541520	1.00[CEU][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]
rs7541703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
7	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
9	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv2465	chr1:113731589-113776605	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12145713	TRAT1	trans	lymphoblastoid	seeQTL
rs12145713	CD99	trans	lymphoblastoid	seeQTL
rs12145713	CXCL14	trans	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113733400-113745200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:113734200-113740800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:113734800-113741400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:113735000-113742400	Weak transcription	K562	blood
5	chr1:113736200-113741000	Weak transcription	Lung	lung
6	chr1:113738000-113741800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:113738600-113740000	Enhancers	Esophagus	oesophagus
8	chr1:113738800-113741200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr1:113738800-113742400	Weak transcription	Fetal Intestine Small	intestine
10	chr1:113738800-113742600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:113738800-113745400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:113739000-113740000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr1:113739400-113740000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr1:113739800-113741600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:113739800-113742400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:113739800-113742400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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