Variant report

Variant	rs3746886
Chromosome Location	chr21:40685598-40685599
allele	A/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	POLR2A	chr21:40685288-40687099	SK-N-MC	brain:	n/a	n/a
2	FOXM1	chr21:40685549-40686078	ECC-1	luminal epithelium:	n/a	n/a
3	E2F6	chr21:40685284-40686675	H1-hESC	embryonic stem cell:	n/a	chr21:40685427-40685439 chr21:40685548-40685557 chr21:40685550-40685560
4	ELK1	chr21:40685518-40686075	GM12878	blood:	n/a	n/a
5	MYC	chr21:40685539-40685939	MCF10A-Er-Src	breast:	n/a	n/a
6	YY1	chr21:40685384-40685947	HepG2	liver:	n/a	chr21:40685765-40685776
7	POLR2A	chr21:40684951-40686864	ProgFib	skin:	n/a	n/a
8	NFIC	chr21:40685380-40685936	HepG2	liver:	n/a	n/a
9	POLR2A	chr21:40685298-40686961	GM12878	blood:	n/a	n/a
10	POLR2A	chr21:40684903-40686876	K562	blood:	n/a	n/a
11	POLR2A	chr21:40685164-40686821	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr21:40685074-40686979	K562	blood:	n/a	n/a
13	TCF12	chr21:40685476-40685844	A549	lung:	n/a	n/a
14	YY1	chr21:40685362-40686070	NT2-D1	testis:	n/a	chr21:40685765-40685776
15	TEAD4	chr21:40685377-40686193	K562	blood:	n/a	n/a
16	MYC	chr21:40685389-40686106	HepG2	liver:	n/a	n/a
17	UBTF	chr21:40684951-40686805	K562	blood:	n/a	n/a
18	SPI1	chr21:40685438-40685686	K562	blood:	n/a	n/a
19	POLR2A	chr21:40685320-40686932	K562	blood:	n/a	n/a
20	CHD2	chr21:40685053-40686356	K562	blood:	n/a	chr21:40685430-40685440 chr21:40685423-40685433
21	POU2F2	chr21:40685309-40686892	GM12878	blood:	n/a	chr21:40685864-40685876 chr21:40685768-40685780 chr21:40685867-40685879
22	POLR2A	chr21:40685344-40686332	HepG2	liver:	n/a	n/a
23	TAF1	chr21:40685361-40685980	PFSK-1	brain:	n/a	n/a
24	YY1	chr21:40685282-40686074	GM12878	blood:	n/a	chr21:40685765-40685776
25	EGR1	chr21:40685268-40686097	ECC-1	luminal epithelium:	n/a	chr21:40685338-40685351 chr21:40685341-40685350 chr21:40685868-40685881
26	NR2F2	chr21:40685546-40686273	K562	blood:	n/a	n/a
27	TBP	chr21:40685371-40686719	H1-hESC	embryonic stem cell:	n/a	n/a
28	TRIM28	chr21:40685344-40686077	K562	blood:	n/a	n/a
29	RELA	chr21:40685304-40686773	GM15510	blood:	n/a	n/a
30	POLR2A	chr21:40685276-40686122	GM12892	blood:	n/a	n/a
31	REST	chr21:40685383-40686047	A549	lung:	n/a	n/a
32	MYC	chr21:40685305-40686158	K562	blood:	n/a	chr21:40685337-40685347
33	E2F4	chr21:40685026-40686759	K562	blood:	n/a	chr21:40685109-40685119 chr21:40685427-40685439 chr21:40685548-40685557 chr21:40685141-40685151 chr21:40685550-40685560 chr21:40685111-40685120
34	KAP1	chr21:40685558-40685968	U2OS	brain:	n/a	n/a
35	PBX3	chr21:40685386-40686032	A549	lung:	n/a	n/a
36	PML	chr21:40685283-40686737	MCF-7	breast:	n/a	n/a
37	RCOR1	chr21:40685534-40686585	GM12878	blood:	n/a	n/a
38	BACH1	chr21:40685595-40685978	K562	blood:	n/a	n/a
39	MYC	chr21:40685342-40686226	K562	blood:	n/a	n/a
40	ZNF143	chr21:40685459-40686713	H1-hESC	embryonic stem cell:	n/a	chr21:40685866-40685884
41	CCNT2	chr21:40684902-40686697	K562	blood:	n/a	chr21:40685051-40685060 chr21:40685265-40685274 chr21:40685765-40685774
42	TCF12	chr21:40685299-40686459	ECC-1	luminal epithelium:	n/a	n/a
43	EP300	chr21:40685315-40686005	ECC-1	luminal epithelium:	n/a	chr21:40685864-40685880 chr21:40685854-40685870 chr21:40685744-40685760 chr21:40685857-40685873
44	POLR2A	chr21:40685154-40686915	HL-60	blood:	n/a	n/a
45	POLR2A	chr21:40685252-40686938	GM12891	blood:	n/a	n/a
46	TAF1	chr21:40685159-40686278	ECC-1	luminal epithelium:	n/a	n/a
47	SIN3AK20	chr21:40684015-40687111	MCF-7	breast:	n/a	n/a
48	ETS1	chr21:40685353-40686016	K562	blood:	n/a	chr21:40685763-40685774
49	MYC	chr21:40685431-40685940	MCF-7	breast:	n/a	n/a
50	YY1	chr21:40685384-40685891	H1-hESC	embryonic stem cell:	n/a	chr21:40685765-40685776

No.	Distal block	Cell Line	Cell type
1	chr21:40683319..40690926-chr21:40755872..40762716,23	MCF-7	breast:
2	chr1:149858125..149858824-chr21:40685009..40685850,2	Hela-S3	cervix:
3	chr21:40554013..40557423-chr21:40684520..40688084,3	MCF-7	breast:
4	chr19:33863948..33864786-chr21:40685269..40686182,2	Hela-S3	cervix:
5	chr21:37527438..37529025-chr21:40684261..40686264,2	MCF-7	breast:
6	chr21:40685228..40687774-chr21:40751832..40753804,3	K562	blood:
7	chr21:40684209..40686276-chr21:40817224..40819799,4	MCF-7	breast:
8	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
9	chr21:40683717..40685708-chr21:40747929..40750593,3	MCF-7	breast:
10	chr21:40683837..40687545-chr21:40816624..40819639,6	K562	blood:
11	chr21:40681416..40687854-chr21:40744378..40751195,8	K562	blood:
12	chr1:204379398..204382038-chr21:40683560..40686325,2	MCF-7	breast:
13	chr21:40683876..40687631-chr21:40749667..40753921,6	K562	blood:
14	chr20:50349937..50351852-chr21:40684525..40686487,2	MCF-7	breast:
15	chr21:40683271..40692626-chr21:40743960..40754349,22	MCF-7	breast:
16	chr21:40684466..40689800-chr21:40758261..40763098,10	K562	blood:
17	chr21:40684648..40686149-chr3:63849352..63850917,2	MCF-7	breast:
18	chr21:40683646..40687466-chr21:40813293..40816602,5	MCF-7	breast:
19	chr21:40555032..40557155-chr21:40684133..40685858,2	MCF-7	breast:
20	chr21:40550424..40553042-chr21:40683249..40686279,3	K562	blood:
21	chr21:40682856..40693378-chr21:40754350..40765471,56	MCF-7	breast:
22	chr21:40683489..40689074-chr21:40750757..40754639,9	MCF-7	breast:
23	chr21:40684332..40690368-chr21:40756970..40764337,16	K562	blood:
24	chr21:40684444..40687629-chr3:63848425..63851169,6	MCF-7	breast:
25	chr21:40684138..40686385-chr9:131445458..131447217,2	MCF-7	breast:
26	chr21:40684582..40688018-chr21:40762846..40766549,4	MCF-7	breast:
27	chr21:40684107..40685647-chr21:40816624..40819498,2	K562	blood:
28	chr21:40553454..40557456-chr21:40682892..40687176,12	K562	blood:

Variant related genes	Relation type
BRWD1-AS1	TF binding region
BRWD1	TF binding region
ENSG00000185437	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000252915	Chromatin interaction
ENSG00000163634	Chromatin interaction
ENSG00000163635	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000119335	Chromatin interaction
ENSG00000153879	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000158615	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000236830	Chromatin interaction
ENSG00000215444	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000238556	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11702268	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11910705	0.85[ASN][1000 genomes]
rs11910906	0.84[ASN][1000 genomes]
rs11910971	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1541100	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1541101	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1888488	0.84[ASN][1000 genomes]
rs1984748	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2026266	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2142117	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2183574	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2183575	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2183576	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2272576	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272577	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2272578	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2297258	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2410121	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836981	0.83[ASN][1000 genomes]
rs34240248	0.86[ASN][1000 genomes]
rs34436313	0.86[ASN][1000 genomes]
rs35182074	0.86[ASN][1000 genomes]
rs3746885	0.99[ASN][1000 genomes]
rs4624474	0.82[ASN][1000 genomes]
rs4816619	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4816623	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4818004	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4818006	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4818007	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4818011	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4818012	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4818014	0.85[ASN][1000 genomes]
rs4818017	0.83[ASN][1000 genomes]
rs61300849	0.86[ASN][1000 genomes]
rs6517529	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6517530	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6517531	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6517532	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6517534	0.82[ASN][1000 genomes]
rs6517536	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6517537	0.86[ASN][1000 genomes]
rs6517539	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6517540	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6517541	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs718225	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7275773	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7276559	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7276698	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7279558	0.83[ASN][1000 genomes]
rs7280149	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7282724	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7282947	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7283439	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7283652	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8127391	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8127986	0.82[ASN][1000 genomes]
rs8128118	0.84[ASN][1000 genomes]
rs8129847	0.84[ASN][1000 genomes]
rs8130099	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8130774	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8131067	0.82[ASN][1000 genomes]
rs8131091	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8131150	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8131263	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8131307	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8132230	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs914157	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs971229	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs973521	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9975562	0.82[ASN][1000 genomes]
rs9975614	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9978591	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9978953	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9979547	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9981301	0.86[ASN][1000 genomes]
rs9981656	0.88[EUR][1000 genomes];0.96[ASN][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	nsv459259	chr21:40571246-40701169	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv587480	chr21:40571246-40701169	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3429298	chr21:40670131-40688774	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
5	esv3439649	chr21:40683507-40687455	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv1059420	chr21:40684295-40745952	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
7	nsv587482	chr21:40684427-40706594	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40683600-40686600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr21:40683800-40686400	Active TSS	Thymus	Thymus
3	chr21:40684000-40685800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr21:40684000-40686200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
5	chr21:40684000-40686200	Active TSS	Fetal Thymus	thymus
6	chr21:40684000-40686400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr21:40684000-40686400	Active TSS	Right Ventricle	heart
8	chr21:40684000-40686600	Active TSS	H1 Cell Line	embryonic stem cell
9	chr21:40684000-40686600	Active TSS	Aorta	Aorta
10	chr21:40684000-40686600	Active TSS	Sigmoid Colon	Sigmoid Colon
11	chr21:40684200-40685600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr21:40684200-40686000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr21:40684200-40686000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr21:40684200-40686000	Active TSS	Placenta Amnion	Placenta Amnion
15	chr21:40684200-40686000	Active TSS	HepG2	liver
16	chr21:40684200-40686200	Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr21:40684200-40686200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr21:40684200-40686200	Active TSS	Brain Anterior Caudate	brain
19	chr21:40684200-40686200	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr21:40684200-40686400	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr21:40684200-40686400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr21:40684200-40686400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr21:40684200-40686400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr21:40684200-40686400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr21:40684200-40686400	Active TSS	Brain Cingulate Gyrus	brain
26	chr21:40684200-40686400	Active TSS	Fetal Brain Female	brain
27	chr21:40684200-40686400	Active TSS	Pancreas	Pancrea
28	chr21:40684200-40686400	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr21:40684200-40686400	Active TSS	GM12878-XiMat	blood
30	chr21:40684200-40686600	Active TSS	H9 Cell Line	embryonic stem cell
31	chr21:40684200-40686600	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr21:40684200-40686600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr21:40684200-40686600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr21:40684200-40686600	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr21:40684200-40686600	Active TSS	Fetal Intestine Large	intestine
36	chr21:40684200-40686600	Active TSS	Fetal Intestine Small	intestine
37	chr21:40684200-40686600	Active TSS	Fetal Stomach	stomach
38	chr21:40684200-40686600	Active TSS	Left Ventricle	heart
39	chr21:40684200-40686600	Active TSS	Ovary	ovary
40	chr21:40684200-40686600	Active TSS	Psoas Muscle	Psoas
41	chr21:40684200-40686600	Active TSS	Stomach Smooth Muscle	stomach
42	chr21:40684200-40686600	Active TSS	HSMM	muscle
43	chr21:40684200-40686800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr21:40684200-40686800	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr21:40684400-40685600	Weak transcription	Stomach Mucosa	stomach
46	chr21:40684400-40686000	Active TSS	Primary hematopoietic stem cells	blood
47	chr21:40684400-40686000	Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr21:40684400-40686000	Active TSS	HMEC	breast
49	chr21:40684400-40686000	Active TSS	HUVEC	blood vessel
50	chr21:40684400-40686000	Active TSS	Monocytes-CD14+_RO01746	blood

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