Variant report

Variant	rs2119483
Chromosome Location	chr6:13406660-13406661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13405977..13407729-chr6:13485216..13487161,3	MCF-7	breast:
2	chr6:13400278..13401808-chr6:13406310..13408265,2	MCF-7	breast:
3	chr6:13405420..13408218-chr6:13438666..13440547,2	K562	blood:
4	chr6:13406137..13408577-chr6:13573927..13576170,2	MCF-7	breast:
5	chr6:13406145..13408180-chr6:13453724..13455818,2	MCF-7	breast:
6	chr6:13395967..13397504-chr6:13405065..13407928,2	K562	blood:

Variant related genes	Relation type
ENSG00000187461	Chromatin interaction
ENSG00000124523	Chromatin interaction
ENSG00000237786	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10807437	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11753720	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754291	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11758233	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1837701	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327673	0.85[EUR][1000 genomes]
rs4145562	1.00[CEU][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs4715251	0.83[CHD][hapmap]
rs478630	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs478804	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs480648	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs485804	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs487607	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs488885	0.80[ASN][1000 genomes]
rs494026	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs500197	0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs500293	0.87[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs513613	0.89[ASN][1000 genomes]
rs519890	0.87[CHB][hapmap]
rs520828	0.83[ASN][1000 genomes]
rs523221	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536916	0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs536998	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs559612	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs563662	0.89[ASN][1000 genomes]
rs564361	0.88[CHB][hapmap]
rs565013	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62385763	0.83[EUR][1000 genomes]
rs62386724	0.83[ASN][1000 genomes]
rs62386725	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62386727	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7742086	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs821298	0.89[ASN][1000 genomes]
rs821300	0.89[ASN][1000 genomes]
rs9296672	0.95[CEU][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs935061	0.83[EUR][1000 genomes]
rs9357720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463764	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9474117	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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
rs2119483	GFOD1	cis	cerebellum	SCAN
rs2119483	C6orf114	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13396200-13407000	Weak transcription	Gastric	stomach
2	chr6:13398200-13406800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:13398400-13407400	Weak transcription	Placenta	Placenta
4	chr6:13399200-13406800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:13401600-13407000	Weak transcription	GM12878-XiMat	blood
6	chr6:13401800-13419000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr6:13403600-13409600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr6:13404000-13407400	Enhancers	Fetal Heart	heart
9	chr6:13404000-13408800	Enhancers	Brain Angular Gyrus	brain
10	chr6:13404000-13409000	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr6:13404200-13407200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:13404400-13407200	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr6:13404400-13407400	Enhancers	A549	lung
14	chr6:13404400-13407800	Enhancers	NHLF	lung
15	chr6:13404400-13408200	Enhancers	Brain Cingulate Gyrus	brain
16	chr6:13404400-13408800	Enhancers	Adipose Nuclei	Adipose
17	chr6:13404400-13408800	Enhancers	Left Ventricle	heart
18	chr6:13404400-13408800	Enhancers	Psoas Muscle	Psoas
19	chr6:13404400-13408800	Enhancers	Right Atrium	heart
20	chr6:13404400-13409000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr6:13404400-13411400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:13404800-13407000	Weak transcription	Fetal Lung	lung
23	chr6:13404800-13408600	Enhancers	Spleen	Spleen
24	chr6:13405000-13407200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:13405000-13407400	Enhancers	Hela-S3	cervix
26	chr6:13405000-13407600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr6:13405000-13410200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:13405000-13418400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr6:13405000-13421800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr6:13405200-13407600	Weak transcription	NHEK	skin
31	chr6:13405200-13408800	Enhancers	Brain Anterior Caudate	brain
32	chr6:13405400-13406800	Weak transcription	HMEC	breast
33	chr6:13405400-13407200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:13405400-13407200	Weak transcription	Osteobl	bone
35	chr6:13405400-13407400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:13405400-13407400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:13405400-13407400	Weak transcription	HSMM	muscle
38	chr6:13405400-13407600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr6:13405400-13407600	Weak transcription	NH-A	brain
40	chr6:13405400-13407800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:13405400-13409800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:13405400-13410400	Weak transcription	Aorta	Aorta
43	chr6:13405600-13407600	Enhancers	K562	blood
44	chr6:13405600-13408600	Enhancers	Fetal Muscle Leg	muscle
45	chr6:13405800-13407000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:13405800-13407200	Enhancers	Stomach Mucosa	stomach
47	chr6:13406000-13408600	Enhancers	Duodenum Mucosa	Duodenum
48	chr6:13406000-13408800	Enhancers	Primary B cells from cord blood	blood
49	chr6:13406000-13408800	Enhancers	Lung	lung
50	chr6:13406000-13408800	Enhancers	Right Ventricle	heart

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