Variant report

Variant	rs1008260
Chromosome Location	chr7:126433327-126433328
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	chr7:126427196..126429754-chr7:126431712..126435448,3	K562	blood:
2	7:126085913-126088095..7:126429477-126435211	GM12878	blood:

Variant related genes	Relation type
ENSG00000179603	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10215498	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs10215590	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs10216287	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs10216314	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10227255	0.85[JPT][hapmap]
rs10227949	0.85[JPT][hapmap]
rs10229765	1.00[JPT][hapmap]
rs10239010	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs10241618	1.00[JPT][hapmap]
rs10250459	0.92[CEU][hapmap];0.81[YRI][hapmap]
rs10252649	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs10254445	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs10254692	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs10257388	0.85[JPT][hapmap]
rs10259217	0.86[JPT][hapmap]
rs10259229	0.86[JPT][hapmap]
rs10271146	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs10487457	0.86[JPT][hapmap]
rs10487459	0.86[JPT][hapmap]
rs10487460	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs10954133	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs11763603	0.92[CEU][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap]
rs11763734	0.92[CEU][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs11765100	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs11768413	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11769307	0.85[JPT][hapmap]
rs11769459	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11769491	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs11770578	0.92[CEU][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs11773772	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12333442	0.92[CEU][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap]
rs12333645	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs12706742	1.00[JPT][hapmap]
rs12706745	0.86[JPT][hapmap]
rs12706746	1.00[JPT][hapmap]
rs12706747	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13222700	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13224779	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs13225829	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13226065	0.96[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13226841	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap]
rs13236505	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs13239613	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13240076	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13240418	0.92[CEU][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13242233	1.00[JPT][hapmap]
rs1361988	1.00[JPT][hapmap]
rs1361995	0.86[JPT][hapmap]
rs1361998	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1361999	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1362000	0.88[CEU][hapmap]
rs1362002	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1362004	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1362005	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1419492	1.00[JPT][hapmap]
rs1419508	0.92[CEU][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs1557646	0.92[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs1592370	0.96[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17150172	0.86[JPT][hapmap]
rs17619947	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17620189	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs17620525	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17626816	0.86[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17627206	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17683174	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17683391	0.85[ASW][hapmap];0.92[CEU][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17693362	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs1946109	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1946114	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs1946115	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs1989849	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1989850	0.96[CEU][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2023733	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2023734	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2023735	0.96[CEU][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2106352	0.85[JPT][hapmap]
rs2106600	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2106601	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs2157753	0.92[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2157977	0.92[CEU][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap]
rs2157978	0.92[CEU][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs2157979	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs2214159	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs2283071	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2283076	0.85[JPT][hapmap]
rs2283079	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs2299501	0.86[JPT][hapmap]
rs2299502	0.85[JPT][hapmap]
rs2299503	0.86[JPT][hapmap]
rs2299505	0.86[JPT][hapmap]
rs2299506	0.86[JPT][hapmap]
rs2299507	0.86[JPT][hapmap]
rs2299508	0.92[CEU][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2299509	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs2299510	0.92[CEU][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap]
rs2299511	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs2299516	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs2299517	0.85[ASW][hapmap];0.92[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2299518	0.91[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2299519	0.92[CEU][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2299520	0.96[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2896376	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs34309246	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35825148	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3808154	0.85[JPT][hapmap]
rs4728053	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4728054	0.82[EUR][1000 genomes]
rs4728055	0.82[EUR][1000 genomes]
rs4731323	1.00[JPT][hapmap]
rs4731330	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731331	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4731332	0.82[EUR][1000 genomes]
rs6467099	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6948500	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6951643	0.96[CEU][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6951771	0.95[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6969572	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs6975541	0.85[JPT][hapmap]
rs6976213	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs727903	0.92[CEU][hapmap]
rs7809518	0.82[JPT][hapmap]
rs886179	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs929175	0.85[JPT][hapmap]
rs929211	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs950789	0.85[JPT][hapmap]
rs954661	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][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
rs1008260	CPA1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:126430800-126433400	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr7:126430800-126433800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr7:126431000-126433600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:126431400-126433800	Enhancers	Brain Cingulate Gyrus	brain
5	chr7:126433200-126433400	Enhancers	Brain Hippocampus Middle	brain
6	chr7:126433200-126433400	Enhancers	Brain Substantia Nigra	brain
7	chr7:126433200-126433800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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