Variant report

Variant	rs3763197
Chromosome Location	chr6:163839012-163839013
allele	A/G
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	ARID3A	chr6:163837789-163839034	K562	blood:	n/a	chr6:163838362-163838378
2	TBL1XR1	chr6:163836856-163839187	K562	blood:	n/a	n/a
3	STAT3	chr6:163838744-163839140	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr6:163838457-163839081	MCF10A-Er-Src	breast:	n/a	chr6:163838660-163838667
5	ZNF384	chr6:163836894-163839662	K562	blood:	n/a	n/a
6	CHD1	chr6:163835594-163839152	IMR90	lung:	n/a	n/a
7	MYC	chr6:163838762-163839054	MCF10A-Er-Src	breast:	n/a	n/a
8	IRF1	chr6:163836838-163839596	K562	blood:	n/a	chr6:163837498-163837512 chr6:163837425-163837441 chr6:163837502-163837512 chr6:163837502-163837516 chr6:163837499-163837516 chr6:163837500-163837513 chr6:163837499-163837513 chr6:163837496-163837510 chr6:163837494-163837514 chr6:163837502-163837513 chr6:163837500-163837513 chr6:163838093-163838100
9	ARID3A	chr6:163837700-163839123	HepG2	liver:	n/a	chr6:163838362-163838378
10	CEBPB	chr6:163838999-163839082	A549	lung:	n/a	chr6:163839031-163839042
11	FOS	chr6:163838723-163839087	MCF10A-Er-Src	breast:	n/a	n/a
12	CUX1	chr6:163837628-163839565	K562	blood:	n/a	chr6:163839091-163839105 chr6:163839088-163839104

No.	Distal block	Cell Line	Cell type
1	chr6:163838578..163840743-chr6:164003751..164005658,2	K562	blood:
2	chr6:163838995..163843341-chr6:163850269..163853237,5	K562	blood:
3	chr6:163836144..163840696-chr6:163983068..163987938,4	K562	blood:
4	chr6:163837764..163839976-chr6:164521625..164524241,2	K562	blood:

Variant related genes	Relation type
CAHM	TF binding region
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11962088	0.94[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11964436	0.87[EUR][1000 genomes]
rs16894934	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16895015	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1737319	0.84[CHD][hapmap];0.80[TSI][hapmap]
rs1737324	0.87[CHD][hapmap];0.80[TSI][hapmap]
rs1737328	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs17591955	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1764010	0.84[CHD][hapmap]
rs2064230	0.81[ASN][1000 genomes]
rs2065857	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2143358	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2294698	0.88[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs2294703	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2294706	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2294707	0.88[ASN][1000 genomes]
rs2294709	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs34979127	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3756879	0.94[CHB][hapmap];0.80[JPT][hapmap]
rs3857504	1.00[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3904720	0.93[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4263561	0.83[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs4709716	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4709717	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs55779730	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56062115	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6455897	0.84[JPT][hapmap]
rs6931903	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6939218	0.86[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs715020	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs73013582	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73013591	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73015309	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73015318	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73015387	0.92[ASN][1000 genomes]
rs7758706	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7772756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9346960	0.89[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs9347760	0.82[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap]
rs9364689	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs9364691	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9364692	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1797109	chr6:163834147-163908115	Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv605209	chr6:163835281-163839012	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3763197	LOC441177	cis	cerebellum	SCAN
rs3763197	QKI	cis	Liver	GTEx
rs3763197	QKI	Cis_1M	lymphoblastoid	RTeQTL
rs3763197	UNC93A	cis	parietal	SCAN
rs3763197	SYNPR	trans	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163832600-163841400	Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr6:163833000-163843400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr6:163833200-163841000	Active TSS	Fetal Muscle Leg	muscle
4	chr6:163833200-163842000	Active TSS	HSMMtube	muscle
5	chr6:163833400-163839400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:163833400-163839400	Active TSS	NH-A	brain
7	chr6:163833400-163839600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:163833400-163839800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:163833400-163839800	Active TSS	Fetal Muscle Trunk	muscle
10	chr6:163833400-163840400	Active TSS	Fetal Brain Female	brain
11	chr6:163833400-163840600	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr6:163833400-163841400	Active TSS	Stomach Smooth Muscle	stomach
13	chr6:163833400-163841400	Active TSS	NHLF	lung
14	chr6:163833400-163843600	Active TSS	Right Ventricle	heart
15	chr6:163833600-163839400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:163833600-163839600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:163833600-163840000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:163833600-163840400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:163833600-163841400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:163833600-163841400	Active TSS	HSMM	muscle
21	chr6:163833600-163842400	Active TSS	Psoas Muscle	Psoas
22	chr6:163833600-163843000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:163833800-163839800	Active TSS	Left Ventricle	heart
24	chr6:163833800-163840000	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr6:163833800-163840800	Active TSS	K562	blood
26	chr6:163833800-163841600	Active TSS	Ovary	ovary
27	chr6:163834000-163840800	Active TSS	GM12878-XiMat	blood
28	chr6:163834200-163839200	Active TSS	Thymus	Thymus
29	chr6:163834200-163839400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:163834200-163839400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:163834200-163841000	Active TSS	HMEC	breast
32	chr6:163834200-163841400	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr6:163835000-163841600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:163836200-163839600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:163836200-163840800	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr6:163836200-163840800	Active TSS	Fetal Heart	heart
37	chr6:163836200-163841400	Active TSS	Brain Anterior Caudate	brain
38	chr6:163836200-163841400	Active TSS	Brain Substantia Nigra	brain
39	chr6:163836200-163843400	Active TSS	Brain Angular Gyrus	brain
40	chr6:163836800-163841400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:163837000-163840400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:163837000-163840600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:163837000-163841400	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr6:163837000-163843400	Active TSS	Right Atrium	heart
45	chr6:163837200-163839200	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr6:163837200-163839400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:163837400-163857200	Weak transcription	Spleen	Spleen
48	chr6:163837800-163840800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:163837800-163840800	Weak transcription	Stomach Mucosa	stomach
50	chr6:163837800-163842000	Active TSS	Brain Cingulate Gyrus	brain

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