Variant report

Variant	rs12571241
Chromosome Location	chr10:98113333-98113334
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	chr10:98104317..98106846-chr10:98113043..98115259,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10218881	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748671	0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10786280	1.00[ASN][1000 genomes]
rs10882772	0.81[CEU][hapmap]
rs10882775	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882779	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10882781	0.81[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11188722	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188726	1.00[ASN][1000 genomes]
rs11188729	1.00[YRI][hapmap]
rs11188730	1.00[YRI][hapmap]
rs11188731	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs11591467	0.81[CEU][hapmap]
rs11593074	0.81[CEU][hapmap]
rs11597348	0.81[CEU][hapmap]
rs12242936	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs12253096	1.00[YRI][hapmap]
rs12254238	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12254673	1.00[YRI][hapmap]
rs12258764	0.89[GIH][hapmap];0.83[MEX][hapmap]
rs12262883	1.00[YRI][hapmap]
rs12570008	0.81[JPT][hapmap]
rs12572329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12766367	0.82[ASW][hapmap]
rs12772674	0.82[ASW][hapmap]
rs17111736	0.81[JPT][hapmap]
rs1923704	1.00[ASN][1000 genomes]
rs1923706	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146390	0.91[GIH][hapmap];0.83[MEX][hapmap]
rs2146392	0.87[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2146393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273891	0.81[CEU][hapmap];0.86[TSI][hapmap]
rs2861572	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs2861574	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789938	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs3814224	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818313	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs4424609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4917732	0.80[CEU][hapmap]
rs7077344	0.81[CEU][hapmap]
rs7085949	1.00[ASN][1000 genomes]
rs7096643	1.00[ASN][1000 genomes]
rs9651412	1.00[YRI][hapmap]
rs9971056	1.00[YRI][hapmap]

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	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active 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	45 gene(s)	inside rSNPs	diseases
2	nsv831950	chr10:98080972-98245434	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12571241	SFRP5	cis	cerebellum	SCAN
rs12571241	CHUK	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98106200-98126000	Weak transcription	Aorta	Aorta
2	chr10:98110800-98114200	Enhancers	Brain Angular Gyrus	brain
3	chr10:98111200-98114200	Enhancers	Fetal Intestine Small	intestine
4	chr10:98111800-98114000	Enhancers	Fetal Intestine Large	intestine
5	chr10:98112400-98113800	Enhancers	Brain Substantia Nigra	brain
6	chr10:98112400-98114000	Enhancers	Duodenum Mucosa	Duodenum
7	chr10:98112600-98114000	Enhancers	Brain Anterior Caudate	brain
8	chr10:98112800-98113400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
9	chr10:98112800-98116800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:98112800-98116800	Weak transcription	Pancreas	Pancrea
11	chr10:98113000-98113400	Bivalent Enhancer	Small Intestine	intestine
12	chr10:98113000-98114000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr10:98113000-98114000	Strong transcription	Thymus	Thymus
14	chr10:98113200-98113400	Flanking Active TSS	Brain Cingulate Gyrus	brain
15	chr10:98113200-98113400	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr10:98113200-98113400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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