Variant report

Variant	rs2572385
Chromosome Location	chr8:11208903-11208904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:11202674..11205995-chr8:11206285..11210798,7	K562	blood:
2	chr8:11208459..11213186-chr8:11213672..11216072,5	K562	blood:
3	chr8:11140914..11143471-chr8:11206296..11209213,2	K562	blood:
4	chr8:11202546..11204675-chr8:11207385..11211000,3	MCF-7	breast:
5	chr8:11205933..11210781-chr8:11211287..11215199,6	K562	blood:

Variant related genes	Relation type
ENSG00000104643	Chromatin interaction
ENSG00000154316	Chromatin interaction
ENSG00000255020	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10110557	0.82[CEU][hapmap]
rs1047950	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10481454	1.00[CHB][hapmap]
rs10503420	1.00[JPT][hapmap]
rs11250130	0.89[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs11250131	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11774569	1.00[CHB][hapmap]
rs11777746	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11781637	0.89[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs11782430	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11784572	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs12547100	0.81[AMR][1000 genomes]
rs12550129	0.81[AMR][1000 genomes]
rs12676062	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12676613	1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12681987	0.89[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap]
rs13260727	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes]
rs13268126	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13274106	0.81[AMR][1000 genomes]
rs1435277	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1435282	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1560971	1.00[CHB][hapmap]
rs17153118	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1865521	0.81[AMR][1000 genomes]
rs2043508	0.80[EUR][1000 genomes]
rs2245232	1.00[CHB][hapmap]
rs2246606	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2249804	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2250028	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2251473	0.93[ASN][1000 genomes]
rs2293859	0.82[CEU][hapmap]
rs2409756	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[AMR][1000 genomes]
rs2572371	0.85[CEU][hapmap]
rs2572382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2572386	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs2572387	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2572397	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2572398	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2572404	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2572452	0.89[CEU][hapmap]
rs2736264	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2736265	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2736266	0.81[EUR][1000 genomes]
rs2736270	0.95[CEU][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2736273	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2736278	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2736282	0.82[CEU][hapmap]
rs2736283	0.82[CEU][hapmap]
rs2736288	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs2736290	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs2736292	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs2736295	0.89[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs2736298	0.80[AMR][1000 genomes]
rs2736311	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34389419	0.83[AMR][1000 genomes]
rs34482136	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34964435	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35009431	0.81[AMR][1000 genomes]
rs35418978	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4363158	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4448232	0.81[AMR][1000 genomes]
rs4841524	0.81[AMR][1000 genomes]
rs4841525	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6601582	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6601584	0.81[AMR][1000 genomes]
rs6601585	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7816606	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7819395	0.82[CEU][hapmap]
rs7828263	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7832747	1.00[JPT][hapmap]
rs7838897	0.82[CEU][hapmap]
rs7839053	0.82[CEU][hapmap]
rs7839307	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv831233	chr8:11046854-11234384	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1033312	chr8:11126800-11252170	Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv1821756	chr8:11169178-11217587	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv890354	chr8:11176147-11266131	Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	esv34097	chr8:11177372-11489894	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv890355	chr8:11202154-11219334	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv890356	chr8:11202154-11223022	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2572385	FLJ10661	cis	cerebellum	SCAN
rs2572385	PRSS55	cis	cerebellum	SCAN
rs2572385	TDH	cis	cerebellum	SCAN
rs2572385	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs2572385	DEFB134	cis	cerebellum	SCAN
rs2572385	MTMR9	Cis_1M	lymphoblastoid	RTeQTL
rs2572385	C8orf79	cis	parietal	SCAN
rs2572385	DEFB136	cis	parietal	SCAN
rs2572385	C8orf48	cis	cerebellum	SCAN
rs2572385	TDH	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11206200-11225000	Weak transcription	Psoas Muscle	Psoas
2	chr8:11206400-11226400	Weak transcription	Brain Anterior Caudate	brain
3	chr8:11207200-11223600	Weak transcription	Brain Hippocampus Middle	brain
4	chr8:11208000-11217600	Weak transcription	Pancreas	Pancrea
5	chr8:11208000-11222400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr8:11208200-11218400	Weak transcription	A549	lung
7	chr8:11208800-11209400	Flanking Active TSS	K562	blood

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