Variant report

Variant	rs7251336
Chromosome Location	chr19:42306326-42306327
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42295737..42298028-chr19:42304935..42307847,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10401370	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10401528	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10401928	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10404939	0.82[CHB][hapmap]
rs10407206	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10407619	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10407797	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10408367	0.85[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10410918	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10414823	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10416824	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10417985	0.82[CHB][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap]
rs10418100	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10419111	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10419827	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10426020	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10426049	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10426243	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10500284	0.92[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs12976571	0.82[CHB][hapmap]
rs12979253	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12984383	0.80[CHB][hapmap]
rs1366610	0.82[CHB][hapmap]
rs1457144	0.82[CHB][hapmap]
rs1811564	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1870092	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.98[TSI][hapmap]
rs1870093	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2008798	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2008808	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2075750	0.82[CHB][hapmap]
rs2075752	0.82[CHB][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap]
rs2075754	0.82[CHB][hapmap]
rs2199829	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2199830	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2290695	0.81[CHB][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap]
rs2305809	0.82[CHB][hapmap];0.82[LWK][hapmap]
rs28821622	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28824227	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28847113	0.86[EUR][1000 genomes]
rs34819714	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3786536	0.82[CHB][hapmap]
rs3786538	0.82[CHB][hapmap]
rs3795022	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3810153	0.82[CEU][hapmap]
rs3922888	0.82[CHB][hapmap]
rs4480913	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4803511	0.82[CHB][hapmap]
rs62117403	0.86[EUR][1000 genomes]
rs6508998	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6508999	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6509000	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7251154	0.89[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7251783	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7251799	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7251960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7254214	0.82[CHB][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap]
rs7258053	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7259967	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs734107	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs734109	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8099934	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8100182	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8104958	0.82[CHB][hapmap]
rs8106505	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8110199	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8113283	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8113538	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8113641	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8113720	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8113741	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8113813	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs873282	0.82[CHB][hapmap]
rs882520	0.82[CEU][hapmap]
rs899662	0.85[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv579615	chr19:42221434-42310388	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7251336	PTGIR	cis	parietal	SCAN
rs7251336	CEACAM3	cis	multi-tissue	Pritchard
rs7251336	EHD2	cis	parietal	SCAN
rs7251336	ZNF473	cis	cerebellum	SCAN
rs7251336	PPP5C	cis	parietal	SCAN
rs7251336	EXOC3L2	cis	cerebellum	SCAN
rs7251336	ZNF575	cis	parietal	SCAN
rs7251336	PSG9	cis	multi-tissue	Pritchard
rs7251336	CEACAM1	cis	cerebellum	SCAN
rs7251336	PSG3	cis	multi-tissue	Pritchard

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42298800-42307400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr19:42301600-42306600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:42303000-42307000	Enhancers	Esophagus	oesophagus
4	chr19:42304800-42316800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr19:42305000-42306600	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr19:42305000-42307000	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr19:42305000-42307200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr19:42305000-42309000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:42305000-42310000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr19:42305200-42307000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:42305200-42307000	Enhancers	Fetal Thymus	thymus
12	chr19:42305200-42308800	Enhancers	Primary B cells from peripheral blood	blood
13	chr19:42305600-42306800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:42305600-42307000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:42305600-42308200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:42305800-42307000	Enhancers	Adipose Nuclei	Adipose
17	chr19:42305800-42308200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr19:42306000-42307200	Enhancers	GM12878-XiMat	blood
19	chr19:42306200-42307000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:42306200-42307200	Flanking Active TSS	Primary hematopoietic stem cells	blood

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