Variant report

Variant	rs3761275
Chromosome Location	chr20:23328865-23328866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr20:23328801-23328867	GM12878	blood:	n/a	n/a
2	IRF3	chr20:23328861-23328971	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:23187473..23190139-chr20:23328538..23331366,2	MCF-7	breast:
2	chr20:23328647..23330996-chr20:23399236..23401652,2	K562	blood:
3	chr20:23112159..23115128-chr20:23328465..23330957,2	K562	blood:

Variant related genes	Relation type
NXT1	TF binding region
ENSG00000233746	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1076776	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12625160	0.84[JPT][hapmap]
rs12625164	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12625999	0.88[JPT][hapmap]
rs12626013	0.84[JPT][hapmap]
rs17757228	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17757442	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17830281	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1936011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277765	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2281428	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2281434	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2295238	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34648279	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3736755	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3746733	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3746737	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3761274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827085	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3827086	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55851398	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56094936	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs56334525	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6036424	0.83[JPT][hapmap]
rs6048803	0.88[JPT][hapmap]
rs6106669	0.83[JPT][hapmap]
rs6114094	0.88[JPT][hapmap]
rs6114142	0.83[JPT][hapmap]
rs6114144	0.83[JPT][hapmap]
rs6132599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132605	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6132606	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6132609	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6132610	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6132617	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6132621	0.84[JPT][hapmap]
rs6132622	0.84[JPT][hapmap]
rs6132623	0.84[JPT][hapmap]
rs6137901	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137907	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6137910	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6137913	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137914	0.86[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137915	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137917	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6137919	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6137920	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6137927	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137929	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137930	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137931	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137936	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137937	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137938	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137939	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137941	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137945	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6137947	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6137948	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6137950	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6137951	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6137957	0.84[JPT][hapmap]
rs6137959	0.84[JPT][hapmap]
rs6137961	0.84[JPT][hapmap]
rs6137975	0.83[JPT][hapmap]
rs761722	0.87[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8183135	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3761275	NXT1	cis	multi-tissue	Pritchard

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23321800-23329400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr20:23325600-23329600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr20:23326000-23329000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr20:23326000-23329800	Weak transcription	Fetal Heart	heart
5	chr20:23326200-23329400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:23326200-23330000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr20:23327000-23330400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr20:23327000-23330800	Weak transcription	Spleen	Spleen
9	chr20:23327200-23330000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr20:23327400-23330000	Weak transcription	HSMM	muscle
11	chr20:23327600-23330000	Weak transcription	Pancreas	Pancrea
12	chr20:23328000-23330000	Enhancers	Placenta Amnion	Placenta Amnion
13	chr20:23328200-23329400	Weak transcription	Fetal Muscle Leg	muscle
14	chr20:23328200-23330000	Weak transcription	Adipose Nuclei	Adipose
15	chr20:23328400-23329400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr20:23328400-23329400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr20:23328600-23329600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr20:23328600-23330000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr20:23328800-23329400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr20:23328800-23329600	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr20:23328800-23330000	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links