Variant report

Variant	rs2144207
Chromosome Location	chr6:149880107-149880108
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	chr6:149865699..149869050-chr6:149878682..149882030,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131013	Chromatin interaction

Extended variants
information (count: 199 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:195)

rs_ID	r²[population]
rs10747275	0.84[EUR][1000 genomes]
rs10747276	0.81[EUR][1000 genomes]
rs10782310	0.83[EUR][1000 genomes]
rs10782311	0.84[EUR][1000 genomes]
rs10782312	0.84[EUR][1000 genomes]
rs10782313	0.84[EUR][1000 genomes]
rs10782314	0.82[EUR][1000 genomes]
rs10782315	0.81[EUR][1000 genomes]
rs10782316	0.81[EUR][1000 genomes]
rs10782317	0.81[EUR][1000 genomes]
rs10782318	0.81[EUR][1000 genomes]
rs1080670	0.84[EUR][1000 genomes]
rs10872643	0.84[EUR][1000 genomes]
rs10872644	0.82[EUR][1000 genomes]
rs10872645	0.83[EUR][1000 genomes]
rs10872646	0.81[EUR][1000 genomes]
rs10872647	0.81[EUR][1000 genomes]
rs10872648	0.81[EUR][1000 genomes]
rs10872649	0.81[EUR][1000 genomes]
rs10872650	0.81[EUR][1000 genomes]
rs11155668	0.84[EUR][1000 genomes]
rs11155669	0.85[EUR][1000 genomes]
rs11155670	0.84[EUR][1000 genomes]
rs11155671	0.86[EUR][1000 genomes]
rs11155674	0.84[EUR][1000 genomes]
rs11155675	0.81[EUR][1000 genomes]
rs11155679	0.81[EUR][1000 genomes]
rs1125	0.84[EUR][1000 genomes]
rs12111376	0.82[EUR][1000 genomes]
rs12174349	0.83[EUR][1000 genomes]
rs12174716	0.86[EUR][1000 genomes]
rs12175504	0.85[EUR][1000 genomes]
rs12178310	0.80[EUR][1000 genomes]
rs12183664	0.85[EUR][1000 genomes]
rs12191643	0.85[EUR][1000 genomes]
rs12193364	0.81[EUR][1000 genomes]
rs12195866	0.88[EUR][1000 genomes]
rs12200670	0.84[EUR][1000 genomes]
rs12201033	0.83[EUR][1000 genomes]
rs12203703	0.83[EUR][1000 genomes]
rs12205092	0.81[EUR][1000 genomes]
rs12206402	0.85[EUR][1000 genomes]
rs12211511	0.86[EUR][1000 genomes]
rs12526675	0.82[EUR][1000 genomes]
rs12528279	0.81[EUR][1000 genomes]
rs12529698	0.86[EUR][1000 genomes]
rs12660304	0.82[EUR][1000 genomes]
rs12662162	0.83[EUR][1000 genomes]
rs12662174	0.85[EUR][1000 genomes]
rs1934534	0.84[EUR][1000 genomes]
rs2064520	0.82[EUR][1000 genomes]
rs2064521	0.84[EUR][1000 genomes]
rs2065663	0.81[EUR][1000 genomes]
rs2185352	0.84[EUR][1000 genomes]
rs2297928	0.83[EUR][1000 genomes]
rs2297930	0.83[EUR][1000 genomes]
rs2297932	0.83[EUR][1000 genomes]
rs34157004	0.84[EUR][1000 genomes]
rs34337297	0.84[EUR][1000 genomes]
rs35031906	0.87[EUR][1000 genomes]
rs35443312	0.87[EUR][1000 genomes]
rs35763894	0.82[EUR][1000 genomes]
rs35830138	0.84[EUR][1000 genomes]
rs35961297	0.84[EUR][1000 genomes]
rs35967444	0.84[EUR][1000 genomes]
rs3763161	0.81[EUR][1000 genomes]
rs3798761	0.84[EUR][1000 genomes]
rs3924871	0.84[EUR][1000 genomes]
rs4039600	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4354168	0.84[EUR][1000 genomes]
rs4380763	0.84[EUR][1000 genomes]
rs4421206	0.84[EUR][1000 genomes]
rs4455682	0.84[EUR][1000 genomes]
rs4869812	0.84[EUR][1000 genomes]
rs4869923	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4870139	0.86[EUR][1000 genomes]
rs4870144	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4870267	0.84[EUR][1000 genomes]
rs4870388	0.84[EUR][1000 genomes]
rs4870493	0.84[EUR][1000 genomes]
rs4870509	0.84[EUR][1000 genomes]
rs4870529	0.83[EUR][1000 genomes]
rs55849538	0.85[EUR][1000 genomes]
rs55938765	0.81[EUR][1000 genomes]
rs55993747	0.84[EUR][1000 genomes]
rs56091542	0.85[EUR][1000 genomes]
rs56397000	0.82[EUR][1000 genomes]
rs57938011	0.85[EUR][1000 genomes]
rs58189451	0.84[EUR][1000 genomes]
rs60424881	0.82[EUR][1000 genomes]
rs62439782	0.84[ASN][1000 genomes]
rs62439811	0.85[EUR][1000 genomes]
rs62439836	0.83[EUR][1000 genomes]
rs62439837	0.84[EUR][1000 genomes]
rs62439840	0.84[EUR][1000 genomes]
rs62439842	0.84[EUR][1000 genomes]
rs62439843	0.87[EUR][1000 genomes]
rs62441279	0.83[EUR][1000 genomes]
rs62441284	0.81[EUR][1000 genomes]
rs66516768	0.84[EUR][1000 genomes]
rs6913486	0.84[EUR][1000 genomes]
rs7450246	0.84[EUR][1000 genomes]
rs7740278	0.85[EUR][1000 genomes]
rs7752594	0.83[EUR][1000 genomes]
rs7753812	0.88[EUR][1000 genomes]
rs7754399	0.84[EUR][1000 genomes]
rs7767622	0.84[EUR][1000 genomes]
rs9027	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9285521	0.82[EUR][1000 genomes]
rs9285522	0.85[EUR][1000 genomes]
rs9285523	0.82[EUR][1000 genomes]
rs9285524	0.88[EUR][1000 genomes]
rs9286597	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9322189	0.83[EUR][1000 genomes]
rs9322192	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9322193	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9322196	0.84[EUR][1000 genomes]
rs9322197	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9322198	0.84[EUR][1000 genomes]
rs9322200	0.85[EUR][1000 genomes]
rs9322204	0.85[EUR][1000 genomes]
rs9322206	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9322207	0.85[EUR][1000 genomes]
rs9322208	0.84[EUR][1000 genomes]
rs9322209	0.84[EUR][1000 genomes]
rs9322210	0.84[EUR][1000 genomes]
rs9322214	0.84[EUR][1000 genomes]
rs9322215	0.86[EUR][1000 genomes]
rs9331657	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9377228	0.82[EUR][1000 genomes]
rs9377229	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9377230	0.84[EUR][1000 genomes]
rs9379348	0.84[EUR][1000 genomes]
rs9383812	0.84[EUR][1000 genomes]
rs9383844	0.83[EUR][1000 genomes]
rs9393132	0.84[EUR][1000 genomes]
rs9393175	0.84[EUR][1000 genomes]
rs9399693	0.81[EUR][1000 genomes]
rs9404047	0.81[EUR][1000 genomes]
rs9404048	0.84[EUR][1000 genomes]
rs9406286	0.85[EUR][1000 genomes]
rs9406345	0.84[EUR][1000 genomes]
rs9406346	0.84[EUR][1000 genomes]
rs9478291	0.82[EUR][1000 genomes]
rs9479094	0.81[EUR][1000 genomes]
rs9479494	0.82[EUR][1000 genomes]
rs9479810	0.84[EUR][1000 genomes]
rs9480009	0.81[EUR][1000 genomes]
rs9480031	0.81[EUR][1000 genomes]
rs9485405	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9485408	0.84[EUR][1000 genomes]
rs9498382	0.80[EUR][1000 genomes]
rs9498384	0.81[EUR][1000 genomes]
rs9505823	0.85[EUR][1000 genomes]
rs9505824	0.85[EUR][1000 genomes]
rs9505826	0.81[EUR][1000 genomes]
rs9505967	0.84[EUR][1000 genomes]
rs9505982	0.84[EUR][1000 genomes]
rs9505983	0.88[EUR][1000 genomes]
rs9688350	0.82[EUR][1000 genomes]
rs9688452	0.84[EUR][1000 genomes]
rs9688517	0.82[EUR][1000 genomes]
rs9688699	0.82[EUR][1000 genomes]
rs9688750	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9688794	0.85[EUR][1000 genomes]
rs9688858	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9688861	0.85[EUR][1000 genomes]
rs9689084	0.85[EUR][1000 genomes]
rs9689340	0.82[EUR][1000 genomes]
rs9689599	0.85[EUR][1000 genomes]
rs9689702	0.82[EUR][1000 genomes]
rs9689716	0.85[EUR][1000 genomes]
rs9689723	0.85[EUR][1000 genomes]
rs9717327	0.81[EUR][1000 genomes]
rs9718079	0.81[EUR][1000 genomes]
rs9766004	0.81[EUR][1000 genomes]
rs9766037	0.83[EUR][1000 genomes]
rs9766886	0.85[EUR][1000 genomes]
rs9767105	0.83[EUR][1000 genomes]
rs9767113	0.83[EUR][1000 genomes]
rs9767123	0.84[EUR][1000 genomes]
rs9767309	0.83[EUR][1000 genomes]
rs9767554	0.83[EUR][1000 genomes]
rs9767555	0.81[EUR][1000 genomes]
rs9767652	0.82[EUR][1000 genomes]
rs9767713	0.82[EUR][1000 genomes]
rs9767727	0.83[EUR][1000 genomes]
rs9800580	0.85[EUR][1000 genomes]
rs9800603	0.85[EUR][1000 genomes]
rs9800614	0.86[EUR][1000 genomes]
rs9800686	0.83[EUR][1000 genomes]
rs9800736	0.84[EUR][1000 genomes]
rs9800806	0.82[EUR][1000 genomes]
rs9800871	0.86[EUR][1000 genomes]
rs9968911	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv966665	chr6:149862756-149895103	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv289	chr6:149864898-149998818	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv5534	chr6:149864898-149998818	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv886762	chr6:149866452-150174507	Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2144207	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs2144207	RP11-350J20.5	cis	Esophagus Mucosa	GTEx
rs2144207	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs2144207	RP11-350J20.5	cis	Artery Tibial	GTEx
rs2144207	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs2144207	GINM1	cis	Whole Blood	GTEx
rs2144207	NUP43	cis	Whole Blood	GTEx
rs2144207	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs2144207	RP11-350J20.5	cis	Thyroid	GTEx
rs2144207	RP11-350J20.5	cis	Adipose Subcutaneous	GTEx
rs2144207	GINM1	cis	Nerve Tibial	GTEx
rs2144207	RP11-350J20.5	cis	Nerve Tibial	GTEx
rs2144207	RP11-350J20.5	cis	lung	GTEx
rs2144207	RP11-350J20.5	cis	Esophagus Muscularis	GTEx
rs2144207	RP11-350J20.5	cis	Stomach	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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