Variant report

Variant	rs4715251
Chromosome Location	chr6:13394411-13394412
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13394396..13395912-chr6:13486331..13488478,2	MCF-7	breast:
2	chr6:13383495..13385578-chr6:13393149..13396280,3	K562	blood:
3	chr6:13345896..13348764-chr6:13394110..13395798,2	MCF-7	breast:
4	chr6:13392824..13395165-chr6:13573638..13575446,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237786	Chromatin interaction
ENSG00000187461	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000124523	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10807437	0.80[CHD][hapmap]
rs1345031	0.88[ASN][1000 genomes]
rs1345032	0.88[ASN][1000 genomes]
rs2119482	0.81[GIH][hapmap]
rs2119483	0.83[CHD][hapmap]
rs2119484	0.96[ASN][1000 genomes]
rs2165419	0.86[GIH][hapmap];0.84[MEX][hapmap]
rs4454121	0.96[ASN][1000 genomes]
rs4715261	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs476138	0.94[ASN][1000 genomes]
rs478630	0.83[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.94[ASN][1000 genomes]
rs478804	0.83[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.94[ASN][1000 genomes]
rs480648	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]
rs485804	0.83[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs488885	0.83[ASN][1000 genomes]
rs490443	0.89[ASN][1000 genomes]
rs494026	0.86[ASN][1000 genomes]
rs500197	0.83[CEU][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs500293	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];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs503117	0.94[ASN][1000 genomes]
rs508153	0.94[ASN][1000 genomes]
rs513613	0.85[ASN][1000 genomes]
rs519657	0.96[ASN][1000 genomes]
rs519890	0.83[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs520828	0.86[ASN][1000 genomes]
rs536916	0.83[CEU][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs536998	0.83[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs546507	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550403	0.90[ASN][1000 genomes]
rs558126	0.93[ASN][1000 genomes]
rs558242	0.94[ASN][1000 genomes]
rs559565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs559612	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs563424	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs563662	0.85[ASN][1000 genomes]
rs564361	0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs565013	0.80[CHD][hapmap]
rs566320	0.96[ASN][1000 genomes]
rs62386724	0.86[ASN][1000 genomes]
rs6458814	0.81[GIH][hapmap]
rs6458815	0.80[GIH][hapmap];0.84[MEX][hapmap]
rs7742086	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs821298	0.85[ASN][1000 genomes]
rs821299	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs821300	0.85[ASN][1000 genomes]
rs9357720	0.83[CHD][hapmap]
rs9474117	0.95[CHD][hapmap];0.82[JPT][hapmap];0.86[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
rs4715251	GFOD1	cis	cerebellum	SCAN
rs4715251	C6orf114	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13368000-13404600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:13376800-13395200	Weak transcription	NHEK	skin
3	chr6:13377800-13395600	Weak transcription	Aorta	Aorta
4	chr6:13381800-13395400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:13382400-13397600	Weak transcription	Esophagus	oesophagus
6	chr6:13383800-13395400	Weak transcription	Brain Anterior Caudate	brain
7	chr6:13384000-13395400	Weak transcription	Brain Substantia Nigra	brain
8	chr6:13384000-13395400	Weak transcription	NHLF	lung
9	chr6:13384200-13395200	Weak transcription	Adipose Nuclei	Adipose
10	chr6:13384200-13395400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:13384200-13395400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:13384200-13395400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:13384600-13395400	Weak transcription	Primary B cells from cord blood	blood
14	chr6:13387000-13395400	Weak transcription	Lung	lung
15	chr6:13387000-13395400	Weak transcription	Right Atrium	heart
16	chr6:13387000-13396000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:13387400-13395400	Weak transcription	Psoas Muscle	Psoas
18	chr6:13390400-13395400	Weak transcription	Pancreas	Pancrea
19	chr6:13391400-13395000	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr6:13391400-13395200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr6:13391400-13395400	Weak transcription	Spleen	Spleen
22	chr6:13392200-13395200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr6:13392400-13394600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr6:13392600-13395400	Weak transcription	Left Ventricle	heart
25	chr6:13393000-13395200	Weak transcription	K562	blood
26	chr6:13393000-13395400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:13393000-13395600	Weak transcription	Right Ventricle	heart
28	chr6:13393200-13395000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:13393200-13395600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:13393200-13395600	Weak transcription	Fetal Heart	heart
31	chr6:13393400-13395400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:13393600-13395400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:13393800-13395400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:13393800-13395400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:13393800-13395400	Weak transcription	HMEC	breast
36	chr6:13394400-13395200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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