Variant report

Variant	rs563424
Chromosome Location	chr6:13396136-13396137
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13396129..13398707-chr6:13570124..13572077,2	MCF-7	breast:
2	chr6:13383495..13385578-chr6:13393149..13396280,3	K562	blood:
3	chr6:13395967..13397504-chr6:13405065..13407928,2	K562	blood:
4	chr6:13370139..13371642-chr6:13395702..13397966,2	K562	blood:

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];0.80[CHD][hapmap]
rs1345031	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1345032	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1550520	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1550521	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2119481	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2119482	0.91[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs2119483	0.87[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs2119484	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165419	0.95[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4454121	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715251	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4715261	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476138	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs478630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[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]
rs478804	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]
rs480648	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]
rs485804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs487607	0.91[CHB][hapmap]
rs488885	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs490443	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs494026	0.89[ASN][1000 genomes]
rs500197	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs500293	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[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503117	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs508153	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs513613	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs519657	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519890	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs520828	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs536916	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs536998	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs544639	0.84[EUR][1000 genomes]
rs546507	0.94[ASN][1000 genomes]
rs550403	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs558126	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs558242	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs559565	0.83[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs559612	1.00[CEU][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs563662	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs564361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565013	0.87[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap]
rs566320	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62386724	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458814	0.95[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs6458815	0.95[CEU][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6910652	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7742086	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs821298	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs821299	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821300	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357720	0.87[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs9370104	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9395768	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9474117	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.89[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
rs563424	C6orf114	cis	cerebellum	SCAN
rs563424	GFOD1	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13368000-13404600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:13382400-13397600	Weak transcription	Esophagus	oesophagus
3	chr6:13394600-13399000	Enhancers	Primary B cells from peripheral blood	blood
4	chr6:13395000-13396600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr6:13395000-13399000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr6:13395200-13396200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:13395200-13396200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:13395200-13396600	Enhancers	HepG2	liver
9	chr6:13395200-13398000	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr6:13395200-13398600	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:13395200-13398800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr6:13395200-13398800	Enhancers	Stomach Mucosa	stomach
13	chr6:13395200-13399000	Enhancers	Primary hematopoietic stem cells	blood
14	chr6:13395200-13399200	Enhancers	Adipose Nuclei	Adipose
15	chr6:13395400-13396200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:13395400-13396200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:13395400-13396200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:13395400-13396200	Enhancers	Brain Cingulate Gyrus	brain
19	chr6:13395400-13396200	Enhancers	Fetal Intestine Small	intestine
20	chr6:13395400-13396200	Enhancers	Fetal Muscle Trunk	muscle
21	chr6:13395400-13396200	Enhancers	Gastric	stomach
22	chr6:13395400-13396200	Flanking Active TSS	Hela-S3	cervix
23	chr6:13395400-13396200	Flanking Active TSS	K562	blood
24	chr6:13395400-13396200	Enhancers	NH-A	brain
25	chr6:13395400-13396200	Enhancers	Osteobl	bone
26	chr6:13395400-13396400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:13395400-13396400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:13395400-13396600	Enhancers	NHDF-Ad	bronchial
29	chr6:13395400-13396800	Enhancers	Brain Substantia Nigra	brain
30	chr6:13395400-13396800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr6:13395400-13396800	Enhancers	NHLF	lung
32	chr6:13395400-13397000	Enhancers	Liver	Liver
33	chr6:13395400-13397000	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr6:13395400-13397000	Enhancers	Fetal Lung	lung
35	chr6:13395400-13397400	Enhancers	Brain Angular Gyrus	brain
36	chr6:13395400-13397400	Enhancers	Brain Anterior Caudate	brain
37	chr6:13395400-13397400	Enhancers	Pancreas	Pancrea
38	chr6:13395400-13397400	Enhancers	Small Intestine	intestine
39	chr6:13395400-13397600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:13395400-13398000	Enhancers	Lung	lung
41	chr6:13395400-13398200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:13395400-13398200	Enhancers	Duodenum Mucosa	Duodenum
43	chr6:13395400-13398400	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr6:13395400-13398400	Enhancers	Right Atrium	heart
45	chr6:13395400-13398600	Enhancers	Primary B cells from cord blood	blood
46	chr6:13395400-13398600	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr6:13395400-13399000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:13395400-13399000	Enhancers	Spleen	Spleen
49	chr6:13395400-13399200	Enhancers	Psoas Muscle	Psoas
50	chr6:13395400-13399200	Enhancers	Skeletal Muscle Male	skeletal muscle

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