Variant report

Variant	rs3001978
Chromosome Location	chr1:152126467-152126468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:152125491..152127414-chr1:152134352..152136756,3	MCF-7	breast:
2	chr1:152124388..152127212-chr1:152139209..152141234,3	MCF-7	breast:
3	chr1:152125198..152127725-chr1:152135136..152137599,3	MCF-7	breast:
4	chr1:152008008..152010475-chr1:152123735..152126708,2	MCF-7	breast:
5	chr1:152126007..152128051-chr1:152155968..152157757,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237975	Chromatin interaction
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10788821	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1131471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1131473	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs11588437	0.95[CHB][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs12033735	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1496036	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]
rs1496041	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2069258	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[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];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2935208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2999563	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3001974	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3007680	0.82[JPT][hapmap]
rs3122305	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3124316	0.95[JPT][hapmap]
rs4579760	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6700989	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs924087	0.84[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]

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	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
7	nsv482125	chr1:152126071-152131704	Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3001978	S100A10	cis	Lymphoblastoid	GTEx
rs3001978	LCE2C	cis	cerebellum	SCAN
rs3001978	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs3001978	THEM4	cis	cerebellum	SCAN
rs3001978	LCE2D	cis	parietal	SCAN
rs3001978	BOLA1	cis	cerebellum	SCAN
rs3001978	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs3001978	S100A10	cis	lymphoblastoid	seeQTL
rs3001978	THEM4	cis	parietal	SCAN
rs3001978	ADAMTSL4	cis	cerebellum	SCAN
rs3001978	S100A10	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152125600-152127400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
2	chr1:152126200-152126800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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