Variant report

Variant	rs7531728
Chromosome Location	chr1:154840516-154840517
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154837856..154840689-chr1:154908471..154910619,2	MCF-7	breast:
2	chr1:154574246..154575826-chr1:154839450..154841062,2	K562	blood:

Variant related genes	Relation type
ENSG00000163344	Chromatin interaction
ENSG00000160710	Chromatin interaction
ENSG00000270361	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1007170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10796934	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10908444	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10908445	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10908446	0.83[ASN][1000 genomes]
rs10908447	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10908448	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs11264276	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11264281	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11264282	0.83[ASN][1000 genomes]
rs11264283	0.83[ASN][1000 genomes]
rs11264284	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12036859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12069356	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12095061	0.91[CEU][hapmap]
rs12130132	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs12144978	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1580943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2061690	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs2102423	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2135219	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2174507	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2335407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2335408	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs2335409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs3738026	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4578216	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs4845398	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845399	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4845400	0.83[ASN][1000 genomes]
rs4845677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845678	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845680	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845681	0.89[EUR][1000 genomes]
rs4845682	0.81[ASN][1000 genomes]
rs4845683	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4845690	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs4845691	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4845693	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs4845695	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs58629129	0.82[AMR][1000 genomes]
rs6656435	0.81[ASN][1000 genomes]
rs6656494	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6669791	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6674853	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6683557	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6699043	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs6699080	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]
rs705094	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs72702224	0.86[AMR][1000 genomes]
rs7528532	0.83[ASN][1000 genomes]
rs7544528	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7553195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs869506	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs877343	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs883718	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs906593	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	nsv464073	chr1:154837796-154904840	Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv547960	chr1:154837796-154904840	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7531728	KCNN3	cis	cerebellum	SCAN
rs7531728	S100A3	cis	cerebellum	SCAN
rs7531728	PBXIP1	cis	lymphoblastoid	seeQTL
rs7531728	LCE2C	cis	cerebellum	SCAN
rs7531728	KCNN3	cis	parietal	SCAN
rs7531728	PBXIP1	Cis_1M	lymphoblastoid	RTeQTL
rs7531728	INTS3	cis	parietal	SCAN
rs7531728	OTUD7B	cis	cerebellum	SCAN
rs7531728	ENSA	cis	parietal	SCAN
rs7531728	RIT1	cis	cerebellum	SCAN
rs7531728	LCE4A	cis	parietal	SCAN
rs7531728	GPATCH4	cis	parietal	SCAN
rs7531728	OAZ3	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154836400-154840600	Enhancers	Spleen	Spleen
2	chr1:154836400-154841600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
3	chr1:154836600-154840600	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr1:154837200-154842200	Active TSS	Colon Smooth Muscle	Colon
5	chr1:154838400-154842400	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr1:154838600-154841600	Weak transcription	Pancreas	Pancrea
7	chr1:154839000-154840600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:154839000-154840800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
9	chr1:154839200-154840600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:154839200-154840800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:154839200-154840800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:154839200-154840800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:154839200-154840800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
14	chr1:154839200-154841000	Enhancers	Lung	lung
15	chr1:154839200-154841200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:154839200-154841600	Active TSS	Brain Substantia Nigra	brain
17	chr1:154839200-154842600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr1:154839200-154843000	Active TSS	Brain Angular Gyrus	brain
19	chr1:154839400-154840600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:154839400-154840800	Enhancers	Fetal Heart	heart
21	chr1:154839400-154841200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:154839600-154840600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr1:154839600-154840600	Active TSS	Brain Anterior Caudate	brain
24	chr1:154839600-154840600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
25	chr1:154839600-154840800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:154839600-154841400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr1:154839600-154841600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
28	chr1:154839600-154842600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr1:154839800-154840600	Active TSS	NH-A	brain
30	chr1:154839800-154841000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:154839800-154841000	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr1:154839800-154841000	Enhancers	Left Ventricle	heart
33	chr1:154839800-154841600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
34	chr1:154839800-154843200	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr1:154840000-154841000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
36	chr1:154840000-154841000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:154840000-154841600	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr1:154840000-154842200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:154840000-154842400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
40	chr1:154840200-154840600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:154840200-154842000	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr1:154840400-154840600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
43	chr1:154840400-154840600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:154840400-154840600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:154840400-154840600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:154840400-154840600	Flanking Active TSS	Right Ventricle	heart
47	chr1:154840400-154840600	Flanking Active TSS	GM12878-XiMat	blood
48	chr1:154840400-154840800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:154840400-154840800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:154840400-154840800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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