Variant report

Variant	rs2572371
Chromosome Location	chr8:11223793-11223794
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11142056..11144386-chr8:11221782..11223912,2	K562	blood:

Variant related genes	Relation type
ENSG00000104643	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10096194	0.92[CEU][hapmap]
rs10098322	0.89[CEU][hapmap]
rs10110557	0.89[CEU][hapmap]
rs1047950	0.89[CEU][hapmap]
rs10503421	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11250129	0.81[CEU][hapmap]
rs11250130	0.82[CEU][hapmap]
rs11777746	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11781637	0.82[CEU][hapmap]
rs11782430	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12549871	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12681987	0.96[CEU][hapmap]
rs1435275	0.80[AMR][1000 genomes]
rs1435277	0.89[CEU][hapmap]
rs17741537	0.92[CEU][hapmap]
rs17797894	0.92[CEU][hapmap]
rs1865521	0.85[AMR][1000 genomes]
rs2043508	0.83[AMR][1000 genomes]
rs2043510	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2060456	0.92[CEU][hapmap]
rs2060457	0.89[CEU][hapmap]
rs2060459	0.92[CEU][hapmap]
rs2246606	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs2249804	0.82[CEU][hapmap]
rs2250028	0.82[CEU][hapmap]
rs2263511	0.82[AMR][1000 genomes]
rs2263512	0.82[AMR][1000 genomes]
rs2293859	0.89[CEU][hapmap]
rs2293860	0.92[CEU][hapmap]
rs2437152	0.80[AMR][1000 genomes]
rs2572379	0.80[AMR][1000 genomes]
rs2572380	0.80[AMR][1000 genomes]
rs2572382	0.85[CEU][hapmap]
rs2572385	0.85[CEU][hapmap]
rs2572386	0.80[AMR][1000 genomes]
rs2572387	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2572389	0.80[AMR][1000 genomes]
rs2572391	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2572394	0.80[AMR][1000 genomes]
rs2572399	0.80[AMR][1000 genomes]
rs2572400	0.80[AMR][1000 genomes]
rs2572450	0.82[AMR][1000 genomes]
rs2572452	0.96[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2736270	0.91[CEU][hapmap]
rs2736278	0.80[EUR][1000 genomes]
rs2736280	0.92[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2736282	0.96[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2736283	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2736285	0.83[AMR][1000 genomes]
rs2736286	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2736287	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2736288	0.83[AMR][1000 genomes]
rs2736290	0.80[AMR][1000 genomes]
rs2736292	0.82[AMR][1000 genomes]
rs2736293	0.80[AMR][1000 genomes]
rs2736294	0.80[AMR][1000 genomes]
rs2736295	0.80[AMR][1000 genomes]
rs2736296	0.80[AMR][1000 genomes]
rs2736297	0.80[AMR][1000 genomes]
rs2736298	0.81[AMR][1000 genomes]
rs2736300	0.80[AMR][1000 genomes]
rs2736302	0.80[AMR][1000 genomes]
rs2736303	0.80[AMR][1000 genomes]
rs2898272	0.82[AMR][1000 genomes]
rs3779891	0.92[CEU][hapmap]
rs4413734	0.92[CEU][hapmap]
rs4448232	0.85[AMR][1000 genomes]
rs4631424	0.80[AMR][1000 genomes]
rs5029571	0.92[CEU][hapmap]
rs57629785	0.80[AMR][1000 genomes]
rs6601582	0.92[CEU][hapmap];0.85[AMR][1000 genomes]
rs6601585	0.82[AMR][1000 genomes]
rs6995404	0.89[CEU][hapmap]
rs7005469	0.92[CEU][hapmap]
rs7016671	0.89[CEU][hapmap]
rs7816606	0.82[AMR][1000 genomes]
rs7819395	0.88[CEU][hapmap]
rs7820301	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7821302	0.80[AMR][1000 genomes]
rs7821459	0.80[AMR][1000 genomes]
rs7828263	0.80[AMR][1000 genomes]
rs7834572	0.80[AMR][1000 genomes]
rs7838897	0.89[CEU][hapmap]
rs7839053	0.89[CEU][hapmap]
rs920044	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
9	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2572371	TDH	cis	cerebellum	SCAN
rs2572371	C8orf48	cis	cerebellum	SCAN
rs2572371	CLDN23	cis	multi-tissue	Pritchard
rs2572371	C8orf79	cis	parietal	SCAN
rs2572371	TDH	cis	parietal	SCAN
rs2572371	PRSS55	cis	cerebellum	SCAN
rs2572371	C8orf13	cis	multi-tissue	Pritchard
rs2572371	FLJ10661	cis	cerebellum	SCAN

Chromatin state (count:17 , 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	chr8:11210000-11224000	Weak transcription	Brain Angular Gyrus	brain
4	chr8:11216000-11227400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr8:11218000-11224000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr8:11218000-11237600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr8:11221000-11224000	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr8:11222400-11225400	Strong transcription	K562	blood
9	chr8:11222600-11224200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr8:11222600-11224400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr8:11222800-11224200	Enhancers	HMEC	breast
12	chr8:11222800-11224400	Enhancers	NHEK	skin
13	chr8:11222800-11226400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr8:11223000-11224400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr8:11223400-11225800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr8:11223400-11225800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr8:11223400-11229000	Weak transcription	Pancreas	Pancrea

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