Variant report

Variant	rs480648
Chromosome Location	chr6:13408874-13408875
allele	C/T
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	USF2	chr6:13407756-13408889	Hela-S3	cervix:	n/a	n/a
2	USF1	chr6:13408487-13408927	ECC-1	luminal epithelium:	n/a	chr6:13408715-13408726
3	USF1	chr6:13408540-13408910	K562	blood:	n/a	chr6:13408715-13408726
4	SMARCC1	chr6:13407342-13408924	Hela-S3	cervix:	n/a	n/a
5	USF1	chr6:13408608-13408919	H1-hESC	embryonic stem cell:	n/a	chr6:13408715-13408726
6	USF1	chr6:13408593-13408920	HepG2	liver:	n/a	chr6:13408715-13408726
7	GATA1	chr6:13407527-13409053	PBDE	blood:	n/a	chr6:13408545-13408552 chr6:13407871-13407880 chr6:13407868-13407878 chr6:13408466-13408476
8	NFIC	chr6:13407747-13409014	ECC-1	luminal epithelium:	n/a	n/a
9	USF1	chr6:13408600-13408911	HepG2	liver:	n/a	chr6:13408715-13408726

No.	Distal block	Cell Line	Cell type
1	chr6:13404530..13406535-chr6:13408392..13410401,3	K562	blood:
2	chr6:13408139..13410381-chr6:13486541..13489029,3	MCF-7	breast:
3	chr6:13408206..13410464-chr6:13614798..13617307,2	MCF-7	breast:
4	chr6:13406818..13408886-chr6:13483840..13488220,5	MCF-7	breast:
5	chr6:13408702..13411029-chr6:13413155..13415071,2	MCF-7	breast:

Variant related genes	Relation type
GFOD1	TF binding region
ENSG00000225921	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000261071	Chromatin interaction
ENSG00000187461	Chromatin interaction
ENSG00000237786	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10807437	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs1345031	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1345032	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1550520	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1550521	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2119481	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2119482	0.91[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs2119483	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2119484	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2165419	0.95[CEU][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4454121	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4715251	0.83[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.94[ASN][1000 genomes]
rs4715261	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs476138	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478630	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478804	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs487607	0.91[CHB][hapmap]
rs488885	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs490443	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs494026	0.87[ASN][1000 genomes]
rs500197	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs500293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs503117	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508153	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513613	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs519657	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs519890	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs520828	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs536916	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs536998	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs544639	0.82[EUR][1000 genomes]
rs546507	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs550403	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs558126	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs558242	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559565	0.83[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs559612	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs563424	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs563662	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs564361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs565013	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs566320	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62386724	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6458814	0.95[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs6458815	0.95[CEU][hapmap];0.90[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6910652	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs7742086	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs821298	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs821299	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs821300	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9357720	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs9370104	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9395768	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9474117	0.91[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs480648	C6orf114	cis	cerebellum	SCAN
rs480648	GFOD1	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13401800-13419000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr6:13403600-13409600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr6:13404000-13409000	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr6:13404400-13409000	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr6:13404400-13411400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:13405000-13410200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:13405000-13418400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:13405000-13421800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:13405400-13409800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:13405400-13410400	Weak transcription	Aorta	Aorta
11	chr6:13406200-13409000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:13406600-13409000	Enhancers	Esophagus	oesophagus
13	chr6:13406800-13409000	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr6:13406800-13409000	Enhancers	HMEC	breast
15	chr6:13408000-13410800	Enhancers	Fetal Heart	heart
16	chr6:13408600-13409000	Enhancers	Brain Cingulate Gyrus	brain
17	chr6:13408600-13409000	Enhancers	K562	blood
18	chr6:13408600-13410200	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:13408600-13411000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:13408600-13411200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:13408600-13411400	Weak transcription	Pancreas	Pancrea
22	chr6:13408600-13411800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:13408600-13412200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:13408600-13412400	Weak transcription	Fetal Lung	lung
25	chr6:13408600-13412400	Weak transcription	Spleen	Spleen
26	chr6:13408600-13412600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:13408600-13412800	Weak transcription	Gastric	stomach
28	chr6:13408600-13413000	Weak transcription	NHLF	lung
29	chr6:13408600-13413200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:13408600-13413200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:13408600-13413200	Weak transcription	Fetal Stomach	stomach
32	chr6:13408600-13413400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:13408600-13413400	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr6:13408600-13413400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:13408600-13413400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:13408600-13413600	Weak transcription	Placenta	Placenta
37	chr6:13408600-13413600	Weak transcription	Osteobl	bone
38	chr6:13408600-13414200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr6:13408600-13414600	Weak transcription	NHEK	skin
40	chr6:13408600-13415800	Enhancers	Liver	Liver
41	chr6:13408600-13422600	Weak transcription	HSMM	muscle
42	chr6:13408800-13409000	Enhancers	A549	lung
43	chr6:13408800-13409000	Enhancers	HSMMtube	muscle
44	chr6:13408800-13409200	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr6:13408800-13409200	Enhancers	Hela-S3	cervix
46	chr6:13408800-13409600	Weak transcription	Brain Angular Gyrus	brain
47	chr6:13408800-13409600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:13408800-13410200	Weak transcription	Brain Hippocampus Middle	brain
49	chr6:13408800-13410200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr6:13408800-13410400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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