Variant report

Variant	rs6458047
Chromosome Location	chr6:38194960-38194961
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38188305..38192389-chr6:38192840..38195857,4	K562	blood:
2	chr6:38193425..38195567-chr6:38201073..38203728,2	K562	blood:
3	chr6:38185221..38187351-chr6:38192774..38196279,3	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1931762	1.00[CHB][hapmap]
rs1931765	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1931766	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2050161	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2395695	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2395696	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4299828	0.94[CEU][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4711527	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4714128	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4714129	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4714130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4714131	1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4714132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4714133	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6458045	0.88[CEU][hapmap]
rs66634926	0.86[AMR][1000 genomes]
rs6904507	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6915783	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6917654	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6924088	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6930118	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6935617	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs726160	1.00[JPT][hapmap]
rs7738411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs873316	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9380722	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9380724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9462416	1.00[JPT][hapmap]
rs9470833	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv522522	chr6:38131442-38207636	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv520053	chr6:38154941-38207636	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6458047	FGD2	cis	cerebellum	SCAN
rs6458047	C6orf129	cis	parietal	SCAN
rs6458047	ZFAND3	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38160800-38201400	Weak transcription	Primary B cells from peripheral blood	blood
2	chr6:38167000-38210400	Weak transcription	Primary T cells from cord blood	blood
3	chr6:38178000-38221600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr6:38178000-38221800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:38181000-38207600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:38181400-38195200	Weak transcription	Colonic Mucosa	Colon
7	chr6:38181400-38202600	Weak transcription	Fetal Stomach	stomach
8	chr6:38181400-38229400	Weak transcription	Fetal Intestine Small	intestine
9	chr6:38183200-38195200	Weak transcription	Fetal Brain Male	brain
10	chr6:38184200-38197200	Weak transcription	HSMMtube	muscle
11	chr6:38184200-38202800	Weak transcription	Psoas Muscle	Psoas
12	chr6:38186600-38215200	Weak transcription	Aorta	Aorta
13	chr6:38188000-38201200	Weak transcription	Spleen	Spleen
14	chr6:38193600-38196200	Enhancers	Brain Substantia Nigra	brain
15	chr6:38193800-38196000	Enhancers	Brain Cingulate Gyrus	brain
16	chr6:38193800-38196000	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr6:38193800-38196200	Enhancers	Brain Hippocampus Middle	brain
18	chr6:38194000-38196000	Enhancers	Brain Angular Gyrus	brain
19	chr6:38194200-38195800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:38194200-38196000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr6:38194200-38196000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:38194200-38200600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:38194200-38200600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:38194400-38199400	Weak transcription	Lung	lung
25	chr6:38194400-38200600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr6:38194400-38230200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:38194600-38200600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:38194800-38195000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:38194800-38195000	Flanking Active TSS	Brain Anterior Caudate	brain

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