Variant report

Variant	rs13123
Chromosome Location	chr8:103839003-103839004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:103836905..103839866-chr8:103851404..103853961,3	MCF-7	breast:
2	chr8:103837792..103839511-chr8:103856236..103858009,2	MCF-7	breast:
3	chr8:103838716..103840356-chr8:103841918..103844695,2	K562	blood:
4	chr8:103838838..103843529-chr8:103874630..103876913,6	K562	blood:

Variant related genes	Relation type
ENSG00000155096	Chromatin interaction
ENSG00000253320	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1019975	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10505040	1.00[CHB][hapmap]
rs12544232	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12546193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12546520	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs12546634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12546636	0.89[AMR][1000 genomes]
rs12547200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12547652	1.00[LWK][hapmap];0.84[MEX][hapmap]
rs12548786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1533182	1.00[LWK][hapmap]
rs17197341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17775390	0.89[AMR][1000 genomes]
rs17775450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17775510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2011262	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2304344	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs2304348	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734066	0.89[AMR][1000 genomes]
rs4734670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4734672	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734674	1.00[LWK][hapmap];0.89[MEX][hapmap]
rs4734676	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4734678	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56854051	0.93[EUR][1000 genomes]
rs62522574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62522576	0.89[AMR][1000 genomes]
rs62522599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62526533	0.87[EUR][1000 genomes]
rs62526534	0.85[EUR][1000 genomes]
rs6998032	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs6999267	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6999525	0.87[EUR][1000 genomes]
rs7016840	1.00[JPT][hapmap]
rs7016962	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1021898	chr8:103767324-103922482	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv465751	chr8:103817106-103894326	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv611822	chr8:103817106-103894326	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv891245	chr8:103838004-103907253	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13123	COX6C	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103823000-103839600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr8:103823000-103841400	Weak transcription	Pancreas	Pancrea
3	chr8:103823000-103855000	Weak transcription	Esophagus	oesophagus
4	chr8:103823200-103841800	Weak transcription	Aorta	Aorta
5	chr8:103823200-103844000	Weak transcription	Right Ventricle	heart
6	chr8:103823200-103853400	Weak transcription	Right Atrium	heart
7	chr8:103823400-103870600	Weak transcription	Stomach Mucosa	stomach
8	chr8:103823600-103839800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr8:103823600-103840000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr8:103825600-103841600	Weak transcription	Lung	lung
11	chr8:103825800-103840200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr8:103826200-103839200	Weak transcription	HUVEC	blood vessel
13	chr8:103826800-103841400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:103826800-103871200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr8:103827000-103839200	Weak transcription	Colon Smooth Muscle	Colon
16	chr8:103827000-103840000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr8:103827200-103839200	Weak transcription	Fetal Lung	lung
18	chr8:103827200-103839400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr8:103827200-103839800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr8:103827200-103840000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr8:103827200-103840000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr8:103827200-103840200	Weak transcription	Fetal Kidney	kidney
23	chr8:103827200-103840400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr8:103827200-103840400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr8:103827200-103840400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr8:103827200-103840800	Weak transcription	Fetal Brain Male	brain
27	chr8:103827800-103844800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr8:103830600-103840000	Weak transcription	HepG2	liver
29	chr8:103830800-103840600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr8:103831600-103840800	Weak transcription	Ovary	ovary
31	chr8:103832000-103840800	Weak transcription	Fetal Heart	heart
32	chr8:103833000-103839800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr8:103833000-103840800	Weak transcription	Brain Substantia Nigra	brain
34	chr8:103833000-103858600	Strong transcription	A549	lung
35	chr8:103833400-103870800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr8:103833600-103848200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr8:103833800-103855200	Weak transcription	Small Intestine	intestine
38	chr8:103834400-103853800	Strong transcription	HSMM	muscle
39	chr8:103834600-103853800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr8:103834600-103856800	Strong transcription	Osteobl	bone
41	chr8:103834600-103867800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr8:103834600-103871200	Strong transcription	K562	blood
43	chr8:103835000-103856600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr8:103835000-103856800	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr8:103835000-103868000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr8:103835000-103871000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr8:103835200-103840400	Weak transcription	Brain Germinal Matrix	brain
48	chr8:103835200-103843000	Strong transcription	NH-A	brain
49	chr8:103835200-103850600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr8:103835200-103856200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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