Variant report

Variant	rs10954138
Chromosome Location	chr7:126425745-126425746
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	chr7:126424654..126426414-chr7:126428939..126431035,2	K562	blood:
2	7:126425074-126429477..7:126751521-126752825	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
ENSG00000179603	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1008907	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10234189	0.81[JPT][hapmap]
rs10251431	0.92[CEU][hapmap]
rs10258445	0.92[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap]
rs10279350	0.82[CHB][hapmap]
rs10487455	0.86[JPT][hapmap]
rs10487456	0.86[JPT][hapmap]
rs10808224	0.86[JPT][hapmap]
rs10808227	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap]
rs10954131	0.86[JPT][hapmap]
rs10954134	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10954135	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11971186	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs11978951	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1204516	0.85[MEX][hapmap];0.84[TSI][hapmap]
rs1204522	0.81[YRI][hapmap]
rs1204526	0.95[MEX][hapmap];0.84[TSI][hapmap]
rs12532564	0.86[JPT][hapmap]
rs12533174	0.86[JPT][hapmap]
rs12533463	0.86[JPT][hapmap]
rs12533543	0.86[JPT][hapmap]
rs12534101	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12537689	0.86[JPT][hapmap]
rs12538680	0.86[JPT][hapmap]
rs12538710	0.86[JPT][hapmap]
rs12538744	0.90[JPT][hapmap]
rs12538796	0.85[JPT][hapmap]
rs12540159	0.90[JPT][hapmap]
rs12666621	0.84[JPT][hapmap]
rs12706744	0.81[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs1361989	0.86[JPT][hapmap]
rs1362001	0.82[CHB][hapmap]
rs1419448	0.92[CEU][hapmap]
rs1419476	0.86[JPT][hapmap]
rs1419479	0.86[JPT][hapmap]
rs1419480	0.86[JPT][hapmap]
rs1419481	0.86[JPT][hapmap]
rs1419484	0.86[JPT][hapmap]
rs1419485	0.90[JPT][hapmap]
rs1419486	0.86[JPT][hapmap]
rs1419487	0.86[JPT][hapmap]
rs1419488	0.86[JPT][hapmap]
rs1419489	0.86[JPT][hapmap]
rs1419493	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1579215	0.85[JPT][hapmap]
rs17610889	0.86[JPT][hapmap]
rs17612358	0.85[JPT][hapmap]
rs17683777	0.85[JPT][hapmap]
rs17684332	0.86[JPT][hapmap]
rs17690706	0.86[JPT][hapmap]
rs1815971	0.86[JPT][hapmap]
rs2027988	0.86[JPT][hapmap]
rs2027989	0.86[JPT][hapmap]
rs2073862	0.86[JPT][hapmap]
rs2106309	0.86[JPT][hapmap]
rs2106310	0.86[JPT][hapmap]
rs2106311	0.85[JPT][hapmap]
rs2106312	0.86[JPT][hapmap]
rs2106313	0.86[JPT][hapmap]
rs2106314	0.86[JPT][hapmap]
rs2157752	0.83[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs2237747	0.86[JPT][hapmap]
rs2237750	0.86[JPT][hapmap]
rs2237751	0.86[JPT][hapmap]
rs2237752	0.86[JPT][hapmap]
rs2237767	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2283070	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2283075	0.92[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs2299475	0.86[JPT][hapmap]
rs2299476	0.86[JPT][hapmap]
rs2299477	0.86[JPT][hapmap]
rs2299478	0.85[JPT][hapmap]
rs2299479	0.86[JPT][hapmap]
rs2299480	0.84[JPT][hapmap]
rs2299484	0.86[JPT][hapmap]
rs2299486	0.90[JPT][hapmap]
rs2299487	0.86[JPT][hapmap]
rs2299488	0.85[JPT][hapmap]
rs2299491	0.86[JPT][hapmap]
rs2299500	0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs2299513	0.81[CHB][hapmap]
rs2299514	0.82[CHB][hapmap]
rs2299521	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2896373	0.81[JPT][hapmap]
rs3802001	0.86[JPT][hapmap]
rs3808145	0.81[EUR][1000 genomes]
rs3808148	0.92[CEU][hapmap]
rs3808156	0.86[JPT][hapmap]
rs3808157	0.86[JPT][hapmap]
rs3808161	0.86[JPT][hapmap]
rs3824018	0.86[JPT][hapmap]
rs3919444	0.82[EUR][1000 genomes]
rs412791	0.91[GIH][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap]
rs4236623	0.85[JPT][hapmap]
rs4236624	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs4380862	0.81[JPT][hapmap]
rs62470209	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6467092	0.86[JPT][hapmap]
rs6963108	0.81[JPT][hapmap]
rs6964806	0.86[JPT][hapmap]
rs6969693	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs6974018	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs6974396	0.84[JPT][hapmap]
rs728600	0.86[JPT][hapmap]
rs728601	0.86[JPT][hapmap]
rs728602	0.86[JPT][hapmap]
rs756900	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7779831	0.80[JPT][hapmap]
rs7780253	0.81[JPT][hapmap]
rs7784073	0.84[CHD][hapmap]
rs7790017	0.86[JPT][hapmap]
rs7792592	0.86[JPT][hapmap]
rs7792700	0.86[JPT][hapmap]
rs7804521	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs886176	0.81[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs9649507	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs975266	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529300	chr7:125669493-126587858	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1032938	chr7:126067684-126587859	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv539119	chr7:126067684-126587859	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv889187	chr7:126219766-126478190	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1032612	chr7:126417533-126456282	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10954138	SLC13A1	cis	cerebellum	SCAN

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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