Variant report

Variant	rs6942364
Chromosome Location	chr6:49462920-49462921
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:49462218-49464476	K562	blood:	n/a	n/a
2	POLR2A	chr6:49461849-49462939	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:49458471..49460387-chr6:49460980..49463015,2	K562	blood:

Variant related genes	Relation type
GLYATL3	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10755760	0.84[AFR][1000 genomes]
rs12190131	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12214753	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1480611	0.86[ASN][1000 genomes]
rs1480612	0.86[ASN][1000 genomes]
rs1480613	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1480615	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1947861	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2061972	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2061973	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2127754	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2127755	0.84[AFR][1000 genomes]
rs2396911	0.84[AFR][1000 genomes]
rs2498470	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2498471	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2498472	0.86[ASN][1000 genomes]
rs2501969	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2501970	0.83[ASN][1000 genomes]
rs2501971	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4367370	0.84[AFR][1000 genomes]
rs4715134	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs7740682	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7757014	0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9296618	0.86[ASN][1000 genomes]
rs9357618	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9367357	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9369904	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9381791	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9381792	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9395499	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9395500	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9463489	0.85[AFR][1000 genomes]
rs9463491	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9463492	0.83[AFR][1000 genomes]
rs9473567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9473568	0.82[CHB][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes]
rs9473582	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1019611	chr6:49431569-49470663	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	nsv885881	chr6:49439805-49575141	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv1793167	chr6:49459978-49466686	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1799212	chr6:49459978-49466791	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6942364	CENPQ	cis	lymphoblastoid	seeQTL
rs6942364	FBXO9	cis	parietal	SCAN
rs6942364	MUT	cis	multi-tissue	Pritchard

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49432000-49463000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr6:49432200-49463800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:49432200-49465000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:49432600-49472000	Weak transcription	NHEK	skin
5	chr6:49440400-49465200	Weak transcription	HUVEC	blood vessel
6	chr6:49441000-49464200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:49448400-49464600	Weak transcription	Gastric	stomach
8	chr6:49449800-49463000	Weak transcription	Lung	lung
9	chr6:49449800-49465000	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:49450400-49464200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:49450600-49464000	Weak transcription	Spleen	Spleen
12	chr6:49451400-49467400	Weak transcription	Fetal Intestine Small	intestine
13	chr6:49451600-49464000	Weak transcription	Fetal Stomach	stomach
14	chr6:49454000-49465200	Weak transcription	Fetal Brain Male	brain
15	chr6:49454800-49463400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr6:49455200-49463600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:49456400-49465000	Weak transcription	HSMMtube	muscle
18	chr6:49456800-49463200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr6:49457000-49464800	Weak transcription	Fetal Kidney	kidney
20	chr6:49457200-49463400	Weak transcription	Aorta	Aorta
21	chr6:49457200-49465000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:49457600-49463800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:49458000-49464200	Weak transcription	Brain Germinal Matrix	brain
24	chr6:49458000-49466600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:49458200-49463400	Weak transcription	Fetal Heart	heart
26	chr6:49458400-49472800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:49458600-49464000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr6:49458600-49464600	Weak transcription	Left Ventricle	heart
29	chr6:49458600-49473800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:49458800-49463000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:49458800-49465000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:49459000-49464200	Weak transcription	Adipose Nuclei	Adipose
33	chr6:49459000-49464400	Weak transcription	Liver	Liver
34	chr6:49459000-49464400	Weak transcription	K562	blood
35	chr6:49459200-49463000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:49460200-49465000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr6:49460400-49463400	Weak transcription	Hela-S3	cervix
38	chr6:49460400-49473200	Weak transcription	HepG2	liver
39	chr6:49460600-49463800	Weak transcription	GM12878-XiMat	blood
40	chr6:49460600-49464000	Weak transcription	Brain Anterior Caudate	brain
41	chr6:49460600-49464200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr6:49460600-49464600	Weak transcription	Brain Hippocampus Middle	brain
43	chr6:49460600-49464800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr6:49460600-49473600	Weak transcription	Stomach Mucosa	stomach
45	chr6:49461000-49463600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr6:49461000-49464200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:49461200-49465200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr6:49461400-49463000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:49461400-49464200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr6:49461400-49472400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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