Variant report

Variant	rs6458065
Chromosome Location	chr6:38641354-38641355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38640160..38642100-chr6:38645505..38647070,2	K562	blood:
2	chr6:38639825..38642602-chr6:38670479..38672378,2	K562	blood:

Variant related genes	Relation type
ENSG00000124767	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10947755	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11966098	0.83[EUR][1000 genomes]
rs13213477	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1623947	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2471999	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3799703	0.96[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs4546477	0.87[EUR][1000 genomes]
rs4599628	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711553	0.81[JPT][hapmap]
rs4714173	0.81[JPT][hapmap]
rs4714175	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]
rs6458063	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66961365	0.84[EUR][1000 genomes]
rs7739414	0.87[EUR][1000 genomes]
rs7750172	0.87[EUR][1000 genomes]
rs7761147	0.87[EUR][1000 genomes]
rs7774816	0.87[EUR][1000 genomes]
rs7775968	0.81[JPT][hapmap]
rs9366969	0.81[JPT][hapmap]
rs9366973	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9369073	0.81[JPT][hapmap]
rs937662	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9380763	0.81[JPT][hapmap]
rs9380765	0.87[EUR][1000 genomes]
rs9380766	0.86[EUR][1000 genomes]
rs9394519	0.81[JPT][hapmap]
rs9462448	0.96[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs9470901	0.81[JPT][hapmap]
rs9470916	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6458065	PRICKLE4	cis	cerebellum	SCAN
rs6458065	GLO1	cis	parietal	SCAN
rs6458065	BYSL	cis	cerebellum	SCAN
rs6458065	GLO1	cis	cerebellum	SCAN
rs6458065	MAPK14	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38609000-38642000	Weak transcription	Primary T cells from cord blood	blood
2	chr6:38609000-38645200	Weak transcription	Fetal Intestine Small	intestine
3	chr6:38609000-38645600	Weak transcription	Left Ventricle	heart
4	chr6:38609200-38642400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:38609200-38643400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:38609400-38642200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:38609600-38642800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:38609800-38643000	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:38612800-38641600	Weak transcription	Adipose Nuclei	Adipose
10	chr6:38612800-38648400	Weak transcription	Brain Anterior Caudate	brain
11	chr6:38612800-38652800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:38613000-38642400	Weak transcription	Fetal Lung	lung
13	chr6:38614800-38654800	Weak transcription	Brain Angular Gyrus	brain
14	chr6:38615200-38642400	Weak transcription	Fetal Brain Female	brain
15	chr6:38615200-38645200	Weak transcription	Ovary	ovary
16	chr6:38615200-38649400	Weak transcription	Fetal Brain Male	brain
17	chr6:38618200-38646200	Weak transcription	Aorta	Aorta
18	chr6:38618800-38643800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:38619200-38642800	Weak transcription	HSMM	muscle
20	chr6:38620200-38646200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:38621000-38643400	Weak transcription	Fetal Kidney	kidney
22	chr6:38621400-38642800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:38621600-38642600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:38621800-38642400	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:38622400-38643200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:38622400-38643800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:38623400-38645600	Weak transcription	Brain Substantia Nigra	brain
28	chr6:38624200-38646200	Weak transcription	Lung	lung
29	chr6:38624600-38643200	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:38624800-38642400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:38625000-38642600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:38626400-38645200	Weak transcription	Fetal Stomach	stomach
33	chr6:38626600-38642400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr6:38629400-38644800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:38631200-38642400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:38637800-38642800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:38638000-38641600	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr6:38638600-38642400	Weak transcription	Fetal Intestine Large	intestine
39	chr6:38639600-38642400	Weak transcription	HepG2	liver
40	chr6:38639800-38642200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:38640000-38641600	Enhancers	GM12878-XiMat	blood
42	chr6:38640000-38643000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr6:38640000-38649400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:38640000-38649400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr6:38640000-38652400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr6:38640200-38642200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:38640200-38642600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:38640200-38650200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr6:38640400-38642400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:38640600-38642200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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