Variant report

Variant	rs657853
Chromosome Location	chr1:146518632-146518633
allele	C/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	NFIC	chr1:146517883-146518822	GM12878	blood:	n/a	n/a
2	FOS	chr1:146517882-146518830	HUVEC	blood vessel:	n/a	chr1:146518066-146518075
3	IRF4	chr1:146518044-146518780	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:146518548-146518878	HUVEC	blood vessel:	n/a	n/a
5	RUNX3	chr1:146518041-146518696	GM12878	blood:	n/a	n/a
6	SP1	chr1:146518446-146518891	GM12878	blood:	n/a	chr1:146518661-146518675
7	POU2F2	chr1:146518480-146518830	GM12891	blood:	n/a	chr1:146518632-146518645 chr1:146518632-146518645 chr1:146518633-146518647 chr1:146518632-146518645
8	POLR2A	chr1:146518555-146518957	SK-N-SH	brain:	n/a	n/a
9	BATF	chr1:146518478-146518756	GM12878	blood:	n/a	n/a
10	EBF1	chr1:146518058-146518657	GM12878	blood:	n/a	n/a
11	EBF1	chr1:146518172-146518653	GM12878	blood:	n/a	n/a
12	POU2F2	chr1:146518405-146518843	GM12878	blood:	n/a	chr1:146518632-146518645 chr1:146518632-146518645 chr1:146518633-146518647 chr1:146518632-146518645
13	RELA	chr1:146517805-146518714	GM12878	blood:	n/a	n/a
14	BATF	chr1:146518484-146518763	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:146512877..146514536-chr1:146516459..146518711,2	K562	blood:

Variant related genes	Relation type
ENSG00000225603	TF binding region
NBPF13P	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10900385	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11240095	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11240110	0.95[ASN][1000 genomes]
rs11578609	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11589576	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1969869	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1969872	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs511131	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs590354	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs594655	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6593794	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428224	chr1:145613243-146553918	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv2757753	chr1:145883119-146697542	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv872251	chr1:146152553-146803630	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
5	nsv872253	chr1:146494246-146548549	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv872254	chr1:146503841-146544721	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
8	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
9	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
10	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
11	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
12	nsv946298	chr1:146510432-146557539	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs657853	NBPF13P	cis	Whole Blood	GTEx
rs657853	RP11-94I2.1	cis	Whole Blood	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146514200-146521400	Enhancers	Primary B cells from cord blood	blood
2	chr1:146514200-146521800	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:146515000-146520400	Enhancers	Primary hematopoietic stem cells	blood
4	chr1:146515800-146519000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:146516800-146520200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:146517400-146519000	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr1:146517400-146519200	Enhancers	NHEK	skin
8	chr1:146517400-146520200	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr1:146517600-146519000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:146517600-146520200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr1:146517800-146519000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:146517800-146519000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:146517800-146519000	Enhancers	HMEC	breast
14	chr1:146517800-146519200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:146517800-146519200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:146517800-146519800	Enhancers	Primary T cells from cord blood	blood
17	chr1:146518400-146518800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr1:146518400-146518800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr1:146518400-146518800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:146518400-146518800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:146518400-146518800	Enhancers	HUVEC	blood vessel
22	chr1:146518400-146518800	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr1:146518400-146519000	Flanking Active TSS	Dnd41	blood
24	chr1:146518400-146519000	Flanking Active TSS	GM12878-XiMat	blood
25	chr1:146518600-146518800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr1:146518600-146519000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:146518600-146519400	Enhancers	Primary T cells fromperipheralblood	blood

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