Variant report

Variant	rs661116
Chromosome Location	chr1:146549635-146549636
allele	A/T
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	BACH1	chr1:146549321-146549737	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr1:146549620-146549668	H1-hESC	embryonic stem cell:	n/a	n/a
3	SUZ12	chr1:146548806-146552743	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:146526066..146527690-chr1:146547733..146550722,2	MCF-7	breast:
2	chr1:145381607..145383149-chr1:146549334..146552301,2	MCF-7	breast:

Variant related genes	Relation type
RNVU1-8	TF binding region
ENSG00000233396	Chromatin interaction
ENSG00000201558	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10157212	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1596236	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17160592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867140	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355379	0.81[ASN][1000 genomes]
rs2477568	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477569	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2584952	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2985722	0.85[ASN][1000 genomes]
rs3011803	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3011808	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011809	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35227958	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4492676	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4494193	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4623760	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs492243	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950301	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950302	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950303	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950355	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950356	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950359	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950360	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950361	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4950362	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950364	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517201	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs535827	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551568	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs556976	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56060937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56359955	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs580852	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs584107	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs590286	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59064267	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604106	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs604716	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs618575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618622	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs630630	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs632334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648937	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593732	0.81[ASN][1000 genomes]
rs6593733	0.81[ASN][1000 genomes]
rs659728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs660096	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs660604	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671690	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs675782	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675809	0.91[ASN][1000 genomes]
rs676288	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678111	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs685741	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs719969	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72704299	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72706414	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72706418	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs942689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9659068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9663073	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs976620	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs976621	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs976622	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs661116	RP11-325P15.1	cis	lung	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146547800-146550000	Enhancers	Liver	Liver
2	chr1:146548600-146551400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:146548800-146551000	Bivalent Enhancer	Right Ventricle	heart
4	chr1:146548800-146551200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
5	chr1:146548800-146551400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:146548800-146551400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
7	chr1:146548800-146552600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr1:146549000-146550000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:146549000-146550200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
10	chr1:146549000-146550400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
11	chr1:146549000-146551000	Enhancers	Primary hematopoietic stem cells	blood
12	chr1:146549000-146551400	Bivalent Enhancer	Fetal Stomach	stomach
13	chr1:146549000-146552600	Bivalent Enhancer	Fetal Brain Male	brain
14	chr1:146549200-146549800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:146549200-146549800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
16	chr1:146549200-146550000	Bivalent Enhancer	Fetal Heart	heart
17	chr1:146549200-146550600	Bivalent Enhancer	Primary B cells from cord blood	blood
18	chr1:146549200-146551400	Enhancers	Pancreas	Pancrea
19	chr1:146549200-146551400	Bivalent Enhancer	Spleen	Spleen
20	chr1:146549200-146552400	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:146549200-146552800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr1:146549400-146549800	Bivalent Enhancer	Brain Substantia Nigra	brain
23	chr1:146549400-146550000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
24	chr1:146549400-146550200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:146549400-146550400	Flanking Bivalent TSS/Enh	NHEK	skin
26	chr1:146549400-146550600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
27	chr1:146549400-146550600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:146549400-146551000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
29	chr1:146549400-146551200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
30	chr1:146549400-146551800	Bivalent Enhancer	Fetal Lung	lung
31	chr1:146549400-146552600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
32	chr1:146549600-146549800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:146549600-146549800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:146549600-146549800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
35	chr1:146549600-146549800	Bivalent Enhancer	Stomach Mucosa	stomach
36	chr1:146549600-146550000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
37	chr1:146549600-146550000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:146549600-146550000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:146549600-146550000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
40	chr1:146549600-146550200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
41	chr1:146549600-146550600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:146549600-146550600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:146549600-146551200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:146549600-146551400	Bivalent Enhancer	Esophagus	oesophagus
45	chr1:146549600-146551800	Bivalent Enhancer	HMEC	breast
46	chr1:146549600-146552800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell

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