Variant report

Variant	rs2293855
Chromosome Location	chr8:11177410-11177411
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	chr8:11177383..11180807-chr8:11181233..11183822,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246477	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10096194	0.92[YRI][hapmap]
rs10098322	1.00[ASW][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs10098488	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs10099569	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10104728	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10110557	0.92[YRI][hapmap]
rs10503418	0.81[TSI][hapmap]
rs11250127	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11250129	0.87[GIH][hapmap];0.83[MEX][hapmap]
rs11774673	0.86[AFR][1000 genomes]
rs11775635	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11781375	0.82[AFR][1000 genomes]
rs11782706	0.92[AFR][1000 genomes]
rs11784458	0.89[AFR][1000 genomes]
rs11784544	0.87[AFR][1000 genomes]
rs11991153	0.82[AFR][1000 genomes]
rs11994376	0.86[AFR][1000 genomes]
rs13253016	0.82[AMR][1000 genomes]
rs13253735	0.81[LWK][hapmap];0.92[YRI][hapmap]
rs13263127	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13270679	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13279067	0.80[EUR][1000 genomes]
rs1347410	0.80[CEU][hapmap]
rs17797443	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1897950	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1897951	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2060459	0.86[YRI][hapmap]
rs2060465	0.81[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2099456	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs2164272	0.81[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2164273	0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2293856	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2572397	0.81[CEU][hapmap]
rs2572398	0.80[CEU][hapmap]
rs2572417	0.81[CEU][hapmap]
rs2572418	0.81[CEU][hapmap]
rs2572419	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2736277	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs28507159	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3174048	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35392635	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35631424	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs35747588	0.80[AFR][1000 genomes]
rs3779891	1.00[ASW][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3808509	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3808513	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3808518	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3808519	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4559208	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4568582	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58283816	0.86[AFR][1000 genomes]
rs6601578	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6601579	0.80[EUR][1000 genomes]
rs6601580	0.89[AFR][1000 genomes]
rs6984759	0.85[EUR][1000 genomes]
rs6985146	0.81[ASW][hapmap];0.96[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6985460	0.81[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6988922	0.88[AFR][1000 genomes]
rs6991074	0.80[EUR][1000 genomes]
rs6991606	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6995404	0.88[CHD][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6996368	0.84[ASN][1000 genomes]
rs7003241	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7004362	0.82[EUR][1000 genomes]
rs7005469	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7016671	1.00[ASW][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs718427	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs7815802	0.82[AFR][1000 genomes]
rs7815804	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7816601	0.87[AFR][1000 genomes]
rs7816636	0.87[AFR][1000 genomes]
rs7817658	0.83[AFR][1000 genomes]
rs7831346	0.89[AFR][1000 genomes]
rs7833966	0.87[AFR][1000 genomes]
rs7834139	0.83[AFR][1000 genomes]
rs7837036	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7838897	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7839053	0.91[YRI][hapmap]

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	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2293855	PRSS55	cis	cerebellum	SCAN
rs2293855	TDH	cis	parietal	SCAN
rs2293855	FLJ10661	cis	cerebellum	SCAN
rs2293855	THEX1	Cis_chr	lymphoblastoid	RTeQTL
rs2293855	C8orf48	cis	cerebellum	SCAN
rs2293855	TDH	cis	cerebellum	SCAN
rs2293855	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs2293855	MTMR9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11154200-11181400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr8:11154200-11183800	Strong transcription	Liver	Liver
3	chr8:11154600-11183000	Strong transcription	Fetal Muscle Trunk	muscle
4	chr8:11155000-11184000	Strong transcription	Dnd41	blood
5	chr8:11155600-11183200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr8:11157200-11180800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr8:11157400-11182600	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr8:11157600-11183000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr8:11160600-11178800	Strong transcription	Fetal Intestine Large	intestine
10	chr8:11161600-11183200	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr8:11161800-11182600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr8:11162000-11180200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr8:11162000-11181200	Strong transcription	HSMM	muscle
14	chr8:11162000-11182600	Strong transcription	Duodenum Mucosa	Duodenum
15	chr8:11162000-11183400	Strong transcription	Primary T cells from cord blood	blood
16	chr8:11162200-11180600	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr8:11162200-11181000	Strong transcription	Placenta	Placenta
18	chr8:11162200-11181600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr8:11162200-11183200	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr8:11162400-11179200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr8:11162400-11179600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr8:11162400-11180600	Strong transcription	Left Ventricle	heart
23	chr8:11162400-11180800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr8:11162400-11182600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr8:11162400-11183000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr8:11162400-11183000	Strong transcription	Adipose Nuclei	Adipose
27	chr8:11162400-11183200	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr8:11162400-11183600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr8:11162400-11183800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr8:11162400-11184000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr8:11162400-11184000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr8:11162400-11184200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr8:11162600-11182800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr8:11162600-11184000	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr8:11164600-11178800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr8:11165400-11181200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr8:11167400-11185200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr8:11167800-11184600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr8:11170000-11179200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr8:11170600-11179200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr8:11170600-11185400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr8:11170800-11180600	Strong transcription	Fetal Muscle Leg	muscle
43	chr8:11170800-11183800	Strong transcription	Primary hematopoietic stem cells	blood
44	chr8:11171000-11183000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr8:11171000-11184200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr8:11171000-11184200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr8:11171200-11183200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr8:11171200-11183400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr8:11171400-11180800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr8:11171600-11191400	Weak transcription	Psoas Muscle	Psoas

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