Variant report

Variant	rs6660721
Chromosome Location	chr1:146771136-146771137
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	chr1:146763180..146767980-chr1:146768468..146771849,4	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10736837	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10751409	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10751410	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10793657	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10793658	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10793661	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10900332	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10900333	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10900336	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11239970	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11239971	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12046626	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1932980	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1932981	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2210954	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3737849	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3737850	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3737853	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3737854	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4264042	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4284292	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4326679	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4385773	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4518968	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6537	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6593756	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6593758	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6593760	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6593761	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6593762	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6593763	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6593764	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6593765	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6593767	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6659630	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6660985	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6665597	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6674987	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6677762	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6678317	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6692355	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6692453	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6697022	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7517324	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7519022	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7525523	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7526996	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7528091	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7528700	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7544598	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7555817	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv872255	chr1:146550780-146969712	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS 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	93 gene(s)	inside rSNPs	diseases
15	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
16	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
17	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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	49 gene(s)	inside rSNPs	diseases
18	nsv1009943	chr1:146618929-146893851	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
19	nsv535132	chr1:146618929-146893851	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
20	nsv437047	chr1:146643555-146841602	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
21	nsv1005809	chr1:146647822-146886419	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
22	nsv535134	chr1:146647822-146886419	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
23	nsv1004849	chr1:146661516-147286826	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
24	nsv535135	chr1:146661516-147286826	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
25	nsv547676	chr1:146686228-146996047	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
26	esv2761654	chr1:146750270-146809156	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
27	nsv872260	chr1:146767353-146826675	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
28	nsv872261	chr1:146767353-146842342	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
29	nsv872262	chr1:146767353-146901677	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6660721	CHD1L	cis	Whole Blood	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146761600-146771400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:146765000-146772600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:146765400-146771400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:146765600-146771600	Weak transcription	Colonic Mucosa	Colon
5	chr1:146766000-146777600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:146766600-146772000	Weak transcription	Fetal Brain Male	brain
7	chr1:146767200-146772000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
8	chr1:146767200-146772200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:146767400-146772200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:146767600-146772200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:146767800-146771200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:146767800-146772200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
13	chr1:146767800-146772400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:146767800-146772400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
15	chr1:146767800-146774600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:146768600-146771200	Weak transcription	Placenta	Placenta
17	chr1:146768600-146771400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:146768600-146772200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:146768800-146771400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:146768800-146771600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:146768800-146772000	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:146768800-146772000	Weak transcription	Right Ventricle	heart
23	chr1:146769000-146771200	Weak transcription	Fetal Intestine Large	intestine
24	chr1:146769000-146771600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:146769000-146771600	Weak transcription	Fetal Thymus	thymus
26	chr1:146769000-146771800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:146769000-146771800	Weak transcription	Fetal Lung	lung
28	chr1:146769000-146772200	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:146769400-146772800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
30	chr1:146769600-146771200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:146769600-146771200	Weak transcription	Left Ventricle	heart
32	chr1:146769600-146771800	Weak transcription	NHDF-Ad	bronchial
33	chr1:146769600-146773400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:146769800-146771200	Weak transcription	Pancreas	Pancrea
35	chr1:146769800-146771400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:146769800-146771600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:146769800-146772600	Weak transcription	Brain Angular Gyrus	brain
38	chr1:146770000-146771200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:146770000-146771200	Weak transcription	Gastric	stomach
40	chr1:146770000-146771200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:146770000-146771200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:146770000-146771400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:146770000-146771400	Weak transcription	Ovary	ovary
44	chr1:146770000-146771600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:146770000-146771600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:146770000-146771600	Weak transcription	Adipose Nuclei	Adipose
47	chr1:146770000-146771600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:146770000-146771800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr1:146770000-146771800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:146770000-146772000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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