Variant report

Variant	rs4714175
Chromosome Location	chr6:38650841-38650842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38650801..38652839-chr6:38670478..38672074,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124767	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10947755	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13213477	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1623947	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2471999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799703	0.85[CEU][hapmap]
rs4599628	0.81[EUR][1000 genomes]
rs6458063	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6458065	0.88[CEU][hapmap];0.86[CHD][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9366973	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9462448	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2758049	chr6:38588969-38711085	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2759421	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv427754	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv428144	chr6:38588969-38711085	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv830642	chr6:38645056-38800657	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4714175	GLO1	cis	parietal	SCAN
rs4714175	BYSL	cis	cerebellum	SCAN
rs4714175	COQ4	trans	cerebellum	SCAN
rs4714175	GLO1	cis	cerebellum	SCAN
rs4714175	MAPK14	cis	parietal	SCAN
rs4714175	PRICKLE4	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38612800-38652800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:38614800-38654800	Weak transcription	Brain Angular Gyrus	brain
3	chr6:38640000-38652400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:38641000-38654800	Weak transcription	Fetal Heart	heart
5	chr6:38641200-38670000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:38641600-38668000	Weak transcription	NHLF	lung
7	chr6:38641800-38651000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr6:38641800-38654800	Weak transcription	Pancreas	Pancrea
9	chr6:38642000-38652600	Weak transcription	Stomach Mucosa	stomach
10	chr6:38642000-38657600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:38642200-38651400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:38642200-38652200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:38642200-38656400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:38642400-38651200	Strong transcription	Fetal Lung	lung
15	chr6:38642400-38652000	Strong transcription	Fetal Muscle Leg	muscle
16	chr6:38642400-38652400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:38642400-38653600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:38642400-38653800	Strong transcription	Dnd41	blood
19	chr6:38642400-38654000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:38642400-38654800	Weak transcription	Psoas Muscle	Psoas
21	chr6:38642400-38655200	Strong transcription	NHEK	skin
22	chr6:38642400-38657000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:38642400-38660000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:38642400-38665600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:38642600-38651800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:38642600-38653400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:38642600-38653600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:38642600-38654600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr6:38642600-38655000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:38642600-38655200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:38642800-38652400	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr6:38642800-38655600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:38642800-38658000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:38642800-38669800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:38643000-38654000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:38643200-38653800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr6:38643200-38656200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:38644400-38651400	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr6:38644400-38653600	Weak transcription	HSMMtube	muscle
40	chr6:38645000-38656600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:38645400-38652200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr6:38646000-38670000	Weak transcription	A549	lung
43	chr6:38646200-38651400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr6:38646400-38652400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:38646600-38651400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:38646600-38651400	Weak transcription	Ovary	ovary
47	chr6:38646600-38656400	Weak transcription	Colonic Mucosa	Colon
48	chr6:38646600-38656400	Weak transcription	Spleen	Spleen
49	chr6:38646600-38663400	Weak transcription	Esophagus	oesophagus
50	chr6:38646800-38653400	Weak transcription	Placenta Amnion	Placenta Amnion

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