Variant report

Variant	rs6699080
Chromosome Location	chr1:154834911-154834912
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	MTA3	chr1:154834579-154838314	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154771337..154773585-chr1:154832415..154834960,2	MCF-7	breast:
2	chr1:154829274..154831457-chr1:154833879..154837058,3	K562	blood:
3	chr1:154827805..154830333-chr1:154834809..154836322,2	MCF-7	breast:
4	chr1:154832792..154836317-chr1:154841340..154844437,3	K562	blood:

Variant related genes	Relation type
KCNN3	TF binding region
ENSG00000143603	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1007170	0.92[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10796934	0.82[AMR][1000 genomes]
rs10908444	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10908445	0.82[AMR][1000 genomes]
rs10908447	0.85[EUR][1000 genomes]
rs10908448	0.85[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs11264276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264281	0.87[EUR][1000 genomes]
rs11264282	0.80[AMR][1000 genomes]
rs11264284	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12036859	0.92[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs12069356	0.82[AMR][1000 genomes]
rs12095061	0.83[CEU][hapmap]
rs12130132	0.80[CEU][hapmap]
rs12144978	0.82[EUR][1000 genomes]
rs1218582	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1580943	0.88[CEU][hapmap];0.80[AMR][1000 genomes]
rs2061690	0.85[CEU][hapmap];0.84[GIH][hapmap]
rs2102423	0.85[CEU][hapmap]
rs2135219	0.81[EUR][1000 genomes]
rs2174507	0.85[CEU][hapmap]
rs2335407	0.92[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2335408	0.85[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs2335409	0.92[CEU][hapmap]
rs3738026	0.85[CEU][hapmap]
rs4845677	0.92[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4845678	0.81[AMR][1000 genomes]
rs4845679	0.92[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs4845680	0.80[AMR][1000 genomes]
rs4845681	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4845683	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4845690	0.85[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs4845691	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4845693	0.85[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs4845695	0.83[CEU][hapmap]
rs6656494	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6669791	0.81[EUR][1000 genomes]
rs6674853	0.83[EUR][1000 genomes]
rs6683557	0.82[AMR][1000 genomes]
rs6699043	0.85[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs705094	0.81[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap]
rs7531728	0.92[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7544528	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7553195	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs869506	0.82[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs877343	0.85[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs883718	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs906593	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv432931	chr1:154794318-154855055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	esv29982	chr1:154818353-154882544	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv432942	chr1:154818353-154903047	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv432964	chr1:154820067-154849590	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv432953	chr1:154820067-154855055	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6699080	OAZ3	cis	parietal	SCAN
rs6699080	PBXIP1	cis	multi-tissue	Pritchard
rs6699080	OTUD7B	cis	cerebellum	SCAN
rs6699080	KCNN3	cis	parietal	SCAN
rs6699080	GPATCH4	cis	parietal	SCAN
rs6699080	PBXIP1	cis	normal skin	skin_eQTL
rs6699080	PBXIP1	Cis_1M	lymphoblastoid	RTeQTL
rs6699080	RIT1	cis	cerebellum	SCAN
rs6699080	S100A3	cis	cerebellum	SCAN
rs6699080	LCE2C	cis	cerebellum	SCAN
rs6699080	INTS3	cis	parietal	SCAN
rs6699080	LCE4A	cis	parietal	SCAN
rs6699080	ENSA	cis	parietal	SCAN
rs6699080	KCNN3	cis	cerebellum	SCAN
rs6699080	UBAP2L	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154821000-154837200	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:154822600-154838000	Weak transcription	Brain Angular Gyrus	brain
3	chr1:154827600-154839400	Enhancers	Fetal Brain Male	brain
4	chr1:154831200-154839800	Enhancers	Psoas Muscle	Psoas
5	chr1:154831400-154839400	Enhancers	Primary B cells from peripheral blood	blood
6	chr1:154831600-154835200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:154831800-154835800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr1:154831800-154839400	Enhancers	Fetal Thymus	thymus
9	chr1:154832000-154837000	Enhancers	HSMM	muscle
10	chr1:154832200-154836600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr1:154832400-154840000	Enhancers	K562	blood
12	chr1:154832800-154835400	Enhancers	Fetal Brain Female	brain
13	chr1:154832800-154835800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:154832800-154836600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:154832800-154837800	Enhancers	HSMMtube	muscle
16	chr1:154833000-154836600	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:154833000-154839200	Weak transcription	Right Atrium	heart
18	chr1:154833200-154835200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:154833200-154835400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:154833200-154835400	Weak transcription	NH-A	brain
21	chr1:154833200-154838400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:154833200-154839800	Weak transcription	Left Ventricle	heart
23	chr1:154833400-154835200	Weak transcription	Right Ventricle	heart
24	chr1:154833400-154835800	Weak transcription	Brain Germinal Matrix	brain
25	chr1:154833400-154836200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:154833400-154836400	Weak transcription	Lung	lung
27	chr1:154833400-154836600	Weak transcription	Brain Substantia Nigra	brain
28	chr1:154833400-154837200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:154833800-154835200	Enhancers	Brain Anterior Caudate	brain
30	chr1:154833800-154837400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:154834000-154836000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:154834200-154835400	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr1:154834200-154836200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:154834200-154836800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:154834400-154835000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:154834400-154835000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:154834400-154835200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
38	chr1:154834400-154835800	Bivalent Enhancer	Fetal Stomach	stomach
39	chr1:154834400-154836400	Weak transcription	Spleen	Spleen
40	chr1:154834400-154836800	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr1:154834400-154837000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:154834600-154835000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:154834600-154835000	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr1:154834600-154837400	Enhancers	Fetal Muscle Leg	muscle
45	chr1:154834800-154835000	Enhancers	Brain Cingulate Gyrus	brain
46	chr1:154834800-154835000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr1:154834800-154835000	Enhancers	Thymus	Thymus
48	chr1:154834800-154835000	Flanking Active TSS	GM12878-XiMat	blood
49	chr1:154834800-154835400	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr1:154834800-154836800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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