Variant report

Variant	rs3808518
Chromosome Location	chr8:11143272-11143273
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:11143156-11143286	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr8:11141037-11143524	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:11142870..11145744-chr8:11152405..11154351,2	K562	blood:
2	chr8:11141582..11144222-chr8:11248890..11251574,2	K562	blood:
3	chr8:11141452..11143588-chr8:11203845..11206287,2	MCF-7	breast:
4	chr8:11141122..11144782-chr8:11147545..11153235,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249316	TF binding region
ENSG00000255020	Chromatin interaction
ENSG00000154316	Chromatin interaction
ENSG00000199368	Chromatin interaction
ENSG00000104643	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10096194	0.85[YRI][hapmap]
rs10098322	1.00[ASW][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs10098488	0.88[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10099569	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10104728	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10107010	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10110557	0.85[YRI][hapmap]
rs10503418	0.81[CEU][hapmap];0.86[TSI][hapmap]
rs11250127	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11250129	0.87[GIH][hapmap]
rs11775635	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11784544	0.81[AFR][1000 genomes]
rs13253735	0.86[LWK][hapmap];0.85[YRI][hapmap]
rs13270679	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13279067	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1435278	0.86[EUR][1000 genomes]
rs17797443	0.92[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1897950	0.92[CEU][hapmap];0.87[CHB][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1897951	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2060465	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2099456	0.92[CEU][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs2164272	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2164273	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2293855	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]
rs2293856	1.00[ASW][hapmap];0.88[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2572397	0.80[CEU][hapmap]
rs2572419	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2736277	0.88[CEU][hapmap];0.86[GIH][hapmap]
rs2736375	0.81[EUR][1000 genomes]
rs28507159	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3174048	0.80[AFR][1000 genomes]
rs35392635	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3779891	1.00[ASW][hapmap];0.89[GIH][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs3808509	0.92[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3808513	1.00[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3808519	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4559208	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4568582	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4840554	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6601578	1.00[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6601579	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6601580	0.80[AFR][1000 genomes]
rs6984759	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6985146	0.92[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs6985460	0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6988922	0.82[AFR][1000 genomes]
rs6991074	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6991606	0.92[CEU][hapmap];0.94[CHB][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6995404	0.82[CHD][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap]
rs7003241	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7004362	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7005469	0.81[CHB][hapmap];0.92[YRI][hapmap]
rs7016671	1.00[ASW][hapmap];0.89[GIH][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs718427	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs765731	0.85[EUR][1000 genomes]
rs7816601	0.81[AFR][1000 genomes]
rs7816636	0.81[AFR][1000 genomes]
rs7831346	0.80[AFR][1000 genomes]
rs7833966	0.81[AFR][1000 genomes]
rs7837036	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7838897	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs7839053	0.83[YRI][hapmap]
rs9286062	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3808518	TDH	cis	cerebellum	SCAN
rs3808518	FLJ10661	cis	cerebellum	SCAN
rs3808518	DEFB134	cis	cerebellum	SCAN
rs3808518	PRSS55	cis	cerebellum	SCAN
rs3808518	CLDN23	cis	multi-tissue	Pritchard
rs3808518	C8orf13	cis	multi-tissue	Pritchard
rs3808518	C8orf48	cis	cerebellum	SCAN
rs3808518	TDH	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11141000-11143400	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr8:11141000-11143400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr8:11141000-11143400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr8:11141000-11143400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr8:11141000-11143400	Active TSS	Psoas Muscle	Psoas
6	chr8:11141000-11143600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr8:11141200-11143400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr8:11141200-11143400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr8:11141200-11143400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr8:11141200-11143400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr8:11141200-11143400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr8:11141200-11143400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr8:11141200-11143600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:11141200-11143600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr8:11141200-11143600	Active TSS	Right Atrium	heart
16	chr8:11141400-11143400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr8:11141400-11143400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr8:11141400-11143600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr8:11141600-11143400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr8:11141600-11143400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr8:11141600-11143400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr8:11141600-11143400	Active TSS	Colon Smooth Muscle	Colon
23	chr8:11141600-11143400	Active TSS	Left Ventricle	heart
24	chr8:11141600-11143600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr8:11141600-11143800	Active TSS	Muscle Satellite Cultured Cells	--
26	chr8:11141600-11143800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr8:11141600-11143800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr8:11141600-11144400	Active TSS	GM12878-XiMat	blood
29	chr8:11141800-11143400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr8:11141800-11143400	Active TSS	Fetal Muscle Trunk	muscle
31	chr8:11141800-11143400	Active TSS	Stomach Smooth Muscle	stomach
32	chr8:11141800-11143400	Active TSS	HMEC	breast
33	chr8:11141800-11143400	Active TSS	HSMM	muscle
34	chr8:11142000-11144000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr8:11142400-11143400	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr8:11142400-11143400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr8:11142400-11144000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr8:11142600-11143400	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr8:11142600-11143400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr8:11142600-11143400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr8:11142600-11143400	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr8:11142600-11143400	Flanking Active TSS	Liver	Liver
43	chr8:11142600-11143400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr8:11142600-11143600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr8:11142800-11143400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr8:11142800-11143400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr8:11142800-11143400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr8:11142800-11143400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr8:11142800-11143400	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr8:11142800-11143400	Flanking Active TSS	Brain Germinal Matrix	brain

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