Variant report

Variant	rs2293860
Chromosome Location	chr8:11219386-11219387
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11212238..11213947-chr8:11218852..11221758,2	MCF-7	breast:
2	chr8:11218476..11220050-chr8:11220905..11223351,2	K562	blood:

Variant related genes	Relation type
ENSG00000154316	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10096194	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10098322	0.96[CEU][hapmap];0.91[GIH][hapmap]
rs10110557	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1047950	0.82[CEU][hapmap]
rs10503421	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11250127	0.84[CEU][hapmap]
rs11250129	0.88[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11250130	0.92[YRI][hapmap];0.83[AMR][1000 genomes]
rs11774673	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11781375	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11781637	0.82[ASW][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs11784458	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11784544	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11991153	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11994376	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12681987	0.89[CEU][hapmap]
rs1435273	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1435277	0.82[CEU][hapmap]
rs17741537	0.91[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17797443	0.82[CEU][hapmap]
rs17797894	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1897950	0.81[CEU][hapmap]
rs1962656	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2060456	1.00[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2060457	0.96[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2060459	0.91[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2060465	0.82[CEU][hapmap]
rs2164272	0.82[CEU][hapmap]
rs2164273	0.82[CEU][hapmap]
rs2293858	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2293859	0.91[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2572371	0.92[CEU][hapmap]
rs2572452	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs2736270	0.82[CEU][hapmap]
rs2736277	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2736280	0.85[CEU][hapmap]
rs2736282	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs2736283	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs34237267	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35687566	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35747588	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3779891	1.00[CEU][hapmap];0.89[GIH][hapmap]
rs3808509	0.82[CEU][hapmap]
rs3808513	0.82[CEU][hapmap]
rs4394351	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4413734	0.91[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4568582	0.81[CEU][hapmap]
rs5029571	1.00[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58283816	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62488721	0.81[EUR][1000 genomes]
rs6601580	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6601582	0.85[CEU][hapmap]
rs6985146	0.82[CEU][hapmap]
rs6985460	0.82[CEU][hapmap]
rs6988922	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6991606	0.82[CEU][hapmap]
rs6995404	0.96[CEU][hapmap];0.87[GIH][hapmap]
rs6997765	0.84[YRI][hapmap]
rs7005469	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7008205	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7016671	0.96[CEU][hapmap];0.89[GIH][hapmap]
rs7815463	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7815802	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7815804	0.81[EUR][1000 genomes]
rs7816601	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7816636	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7817658	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7819395	0.96[CEU][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7820895	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7828711	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7831346	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7833966	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7834139	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7838897	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7839053	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2293860	MTMR9	Cis_1M	lymphoblastoid	RTeQTL
rs2293860	C8orf79	cis	parietal	SCAN
rs2293860	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs2293860	TDH	cis	parietal	SCAN
rs2293860	PRSS55	cis	cerebellum	SCAN
rs2293860	FLJ10661	cis	cerebellum	SCAN
rs2293860	C8orf48	cis	cerebellum	SCAN
rs2293860	TDH	cis	cerebellum	SCAN

Chromatin state (count:26 , 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	chr8:11208000-11222400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr8:11210000-11224000	Weak transcription	Brain Angular Gyrus	brain
6	chr8:11212400-11219400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr8:11212800-11223600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr8:11214600-11221000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr8:11216000-11227400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr8:11216800-11222200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr8:11218000-11224000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr8:11218000-11237600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr8:11218200-11220200	Enhancers	Stomach Mucosa	stomach
14	chr8:11218200-11220800	Weak transcription	K562	blood
15	chr8:11218200-11221400	Weak transcription	Gastric	stomach
16	chr8:11218400-11219600	Weak transcription	Pancreas	Pancrea
17	chr8:11218600-11219600	Flanking Active TSS	HepG2	liver
18	chr8:11218800-11219400	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr8:11218800-11219800	Enhancers	Fetal Intestine Small	intestine
20	chr8:11218800-11220200	Enhancers	Fetal Intestine Large	intestine
21	chr8:11219000-11219800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr8:11219000-11219800	Enhancers	NHEK	skin
23	chr8:11219000-11220200	Flanking Active TSS	A549	lung
24	chr8:11219200-11219600	Enhancers	HMEC	breast
25	chr8:11219200-11219800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr8:11219200-11220000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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