Variant report

Variant	rs551568
Chromosome Location	chr1:146544600-146544601
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:146542036..146544748-chr1:149223441..149225409,2	MCF-7	breast:
2	chr1:146529795..146532554-chr1:146543290..146546177,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206737	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10157212	0.80[EUR][1000 genomes]
rs17160592	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2477568	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2477569	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2477570	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3011808	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3011809	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3011810	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4492676	0.82[EUR][1000 genomes]
rs4494193	0.82[EUR][1000 genomes]
rs4623760	0.82[EUR][1000 genomes]
rs492243	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs493000	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs494122	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4950302	0.84[EUR][1000 genomes]
rs4950354	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4950355	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4950358	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4950359	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4950360	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4950361	0.93[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4950362	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs535827	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs556976	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56060937	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs575115	0.93[CHB][hapmap]
rs584107	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs590286	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59064267	0.83[EUR][1000 genomes]
rs604716	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs618575	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs618622	0.84[EUR][1000 genomes]
rs630630	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs632334	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs632861	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs647596	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs648937	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs659728	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs660096	0.85[EUR][1000 genomes]
rs660604	0.84[EUR][1000 genomes]
rs661116	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs675782	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs676288	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs678111	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs685741	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs719969	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs942689	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9659068	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9663073	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs976621	0.81[EUR][1000 genomes]
rs976622	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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
13	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	111 gene(s)	inside rSNPs	diseases
14	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
15	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
16	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
17	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
18	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs551568	RP11-325P15.1	cis	lung	GTEx
rs551568	CHD1L	cis	Whole Blood	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146543200-146545000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:146543800-146544600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:146543800-146544800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
4	chr1:146543800-146544800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr1:146543800-146544800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr1:146543800-146544800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
7	chr1:146543800-146545000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr1:146543800-146545000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr1:146543800-146545000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:146543800-146545000	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:146543800-146545200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:146543800-146545200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
13	chr1:146544000-146544600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:146544000-146544600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:146544000-146544600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:146544000-146544600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
17	chr1:146544000-146544600	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
18	chr1:146544000-146544600	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
19	chr1:146544000-146544600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:146544000-146544600	Bivalent/Poised TSS	Colonic Mucosa	Colon
21	chr1:146544000-146544600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
22	chr1:146544000-146544600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
23	chr1:146544000-146544600	ZNF genes & repeats	Lung	lung
24	chr1:146544000-146544600	Bivalent Enhancer	Small Intestine	intestine
25	chr1:146544000-146544600	Bivalent Enhancer	Spleen	Spleen
26	chr1:146544000-146544600	Bivalent/Poised TSS	HUVEC	blood vessel
27	chr1:146544000-146544600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
28	chr1:146544000-146544600	Bivalent/Poised TSS	NH-A	brain
29	chr1:146544000-146544800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:146544000-146544800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:146544000-146544800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:146544000-146544800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:146544000-146544800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr1:146544000-146544800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:146544000-146544800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:146544000-146544800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
37	chr1:146544000-146544800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
38	chr1:146544000-146544800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
39	chr1:146544000-146544800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
40	chr1:146544000-146544800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
41	chr1:146544000-146544800	Bivalent/Poised TSS	Fetal Lung	lung
42	chr1:146544000-146544800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
43	chr1:146544000-146544800	Bivalent/Poised TSS	Osteobl	bone
44	chr1:146544000-146545000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
45	chr1:146544000-146545000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:146544000-146545000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
47	chr1:146544000-146545000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
48	chr1:146544000-146545000	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:146544000-146545000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:146544000-146545000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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