Variant report

Variant	rs6932590
Chromosome Location	chr6:27248931-27248932
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	chr6:27203220..27205939-chr6:27245296..27248944,5	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1102568	1.00[CHB][hapmap]
rs11753483	1.00[CHB][hapmap]
rs11755662	1.00[JPT][hapmap]
rs11965377	1.00[CHB][hapmap]
rs11966985	1.00[CHB][hapmap]
rs11967073	1.00[CHB][hapmap]
rs11968996	1.00[JPT][hapmap]
rs11969113	1.00[JPT][hapmap]
rs11969536	1.00[CHB][hapmap]
rs11970095	1.00[CHB][hapmap]
rs11970261	1.00[CHB][hapmap]
rs12664426	1.00[JPT][hapmap]
rs13211166	1.00[JPT][hapmap]
rs16897515	1.00[JPT][hapmap]
rs2893910	1.00[JPT][hapmap]
rs2893912	1.00[CHB][hapmap]
rs35454259	0.88[EUR][1000 genomes]
rs3800316	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs3800318	1.00[JPT][hapmap]
rs3823427	0.85[EUR][1000 genomes]
rs6921711	1.00[JPT][hapmap]
rs6938200	1.00[JPT][hapmap]
rs7744248	1.00[CHB][hapmap]
rs7746199	1.00[JPT][hapmap]
rs7759741	1.00[CHB][hapmap]
rs7760931	1.00[JPT][hapmap]
rs9969094	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	19571808	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6932590	FKSG83	cis	parietal	SCAN
rs6932590	HIST1H2BH	cis	cerebellum	SCAN
rs6932590	HIST1H4L	cis	cerebellum	SCAN
rs6932590	HIST1H3D	cis	parietal	SCAN
rs6932590	BTN3A3	cis	lymphoblastoid	seeQTL
rs6932590	BTN2A1	Cis_1M	lymphoblastoid	RTeQTL
rs6932590	BTN3A2	cis	lymphoblastoid	seeQTL
rs6932590	BTN3A2	cis	Muscle Skeletal	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27247000-27249400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:27247000-27249400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr6:27247200-27249000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:27247200-27249200	Active TSS	H9 Cell Line	embryonic stem cell
5	chr6:27247200-27249200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:27247200-27249400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:27247200-27249400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:27247200-27249400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:27247200-27249400	Active TSS	A549	lung
10	chr6:27247200-27249400	Active TSS	Hela-S3	cervix
11	chr6:27247400-27249200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr6:27247400-27249200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:27247400-27249400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:27247600-27249000	Active TSS	NHDF-Ad	bronchial
15	chr6:27247600-27249000	Flanking Active TSS	Osteobl	bone
16	chr6:27247600-27249200	Active TSS	H1 Cell Line	embryonic stem cell
17	chr6:27247600-27249200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:27247600-27249200	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr6:27247600-27249200	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr6:27247600-27249200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:27247600-27249400	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr6:27247600-27249400	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr6:27247600-27249400	Active TSS	GM12878-XiMat	blood
24	chr6:27247600-27249400	Active TSS	K562	blood
25	chr6:27247800-27249000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:27247800-27249400	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr6:27248000-27249000	Active TSS	HepG2	liver
28	chr6:27248000-27249000	Active TSS	HMEC	breast
29	chr6:27248000-27249200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
30	chr6:27248000-27249200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr6:27248000-27249400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:27248000-27249400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:27248400-27249200	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr6:27248600-27249000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:27248600-27249000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:27248600-27249000	Bivalent Enhancer	Adipose Nuclei	Adipose
37	chr6:27248600-27249200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
38	chr6:27248600-27249400	Active TSS	NHLF	lung
39	chr6:27248600-27255800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:27248800-27249000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:27248800-27249000	Bivalent Enhancer	HUVEC	blood vessel
42	chr6:27248800-27249000	Enhancers	NH-A	brain
43	chr6:27248800-27249000	Flanking Active TSS	NHEK	skin
44	chr6:27248800-27249200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:27248800-27249200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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