Variant report

Variant	rs1496036
Chromosome Location	chr1:152140016-152140017
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	MYC	chr1:152139868-152141462	MCF10A-Er-Src	breast:	n/a	chr1:152140391-152140400
2	MAFK	chr1:152139985-152140786	Hela-S3	cervix:	n/a	n/a
3	STAT3	chr1:152139977-152140757	MCF10A-Er-Src	breast:	n/a	chr1:152140337-152140348 chr1:152140339-152140347
4	STAT3	chr1:152139964-152140751	MCF10A-Er-Src	breast:	n/a	chr1:152140337-152140348 chr1:152140339-152140347
5	ZKSCAN1	chr1:152139847-152140779	Hela-S3	cervix:	n/a	n/a
6	STAT3	chr1:152139983-152140777	MCF10A-Er-Src	breast:	n/a	chr1:152140337-152140348 chr1:152140339-152140347
7	STAT3	chr1:152140009-152140740	MCF10A-Er-Src	breast:	n/a	chr1:152140337-152140348 chr1:152140339-152140347
8	CEBPB	chr1:152139954-152140983	MCF-7	breast:	n/a	n/a
9	FOS	chr1:152140016-152140769	MCF10A-Er-Src	breast:	n/a	n/a
10	MAX	chr1:152139952-152140985	Hela-S3	cervix:	n/a	chr1:152140391-152140400
11	TCF7L2	chr1:152139551-152140976	Hela-S3	cervix:	n/a	n/a
12	CEBPB	chr1:152139989-152140962	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:152138759..152140598-chr1:152141934..152143751,2	MCF-7	breast:
2	chr1:152019311..152021605-chr1:152136763..152140691,3	MCF-7	breast:
3	chr1:152008104..152009692-chr1:152138016..152140338,2	MCF-7	breast:

Variant related genes	Relation type
FLG-AS1	TF binding region
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10788821	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1131471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1131473	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs11588437	0.95[CHB][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs12033735	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1496041	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs2069258	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs2496253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2935208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2999563	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3001974	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3001978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3007680	0.82[JPT][hapmap]
rs3122305	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3124316	0.95[JPT][hapmap]
rs4579760	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4845419	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6700989	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs924087	0.84[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][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	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547853	chr1:152008671-152236760	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv872442	chr1:152054120-152187641	Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1496036	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs1496036	LCE2C	cis	cerebellum	SCAN
rs1496036	BOLA1	cis	cerebellum	SCAN
rs1496036	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs1496036	THEM4	cis	cerebellum	SCAN
rs1496036	S100A10	cis	lymphoblastoid	seeQTL
rs1496036	LCE2D	cis	parietal	SCAN
rs1496036	THEM4	cis	parietal	SCAN
rs1496036	ADAMTSL4	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152131400-152145800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:152134800-152142200	Enhancers	HMEC	breast
3	chr1:152137800-152142800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:152138400-152141400	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr1:152138600-152140600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:152138800-152140400	Weak transcription	GM12878-XiMat	blood
7	chr1:152138800-152141800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:152139200-152141400	Enhancers	HSMMtube	muscle
9	chr1:152139200-152141600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:152139200-152141600	Enhancers	HSMM	muscle
11	chr1:152139400-152140400	Weak transcription	Adipose Nuclei	Adipose
12	chr1:152139400-152141200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr1:152139400-152141400	Enhancers	NHDF-Ad	bronchial
14	chr1:152139400-152142200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:152139400-152142400	Enhancers	NHEK	skin
16	chr1:152139600-152140800	Enhancers	Lung	lung
17	chr1:152139600-152141400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:152139600-152141400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:152139600-152141400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:152139600-152141800	Enhancers	Hela-S3	cervix
21	chr1:152139600-152142200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:152139600-152142200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:152139600-152143200	Enhancers	Esophagus	oesophagus
24	chr1:152139800-152140600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr1:152139800-152140800	Enhancers	Placenta	Placenta
26	chr1:152139800-152141200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:152139800-152141200	Enhancers	NHLF	lung
28	chr1:152139800-152141400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:152139800-152141800	Enhancers	Left Ventricle	heart
30	chr1:152139800-152141800	Enhancers	Osteobl	bone
31	chr1:152139800-152142000	Enhancers	A549	lung
32	chr1:152139800-152142200	Enhancers	NH-A	brain
33	chr1:152140000-152141000	Enhancers	Right Ventricle	heart
34	chr1:152140000-152141400	Enhancers	Spleen	Spleen
35	chr1:152140000-152141800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
36	chr1:152140000-152142400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:152140000-152142400	Enhancers	Right Atrium	heart

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