Variant report

Variant	rs66786953
Chromosome Location	chr3:42641236-42641237
allele	A/C
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	chr3:42641122-42641270	Hela-S3	cervix:	n/a	n/a
2	HA-E2F1	chr3:42640886-42642367	MCF-7	breast:	n/a	chr3:42642320-42642332 chr3:42641918-42641927
3	MAFK	chr3:42641223-42642307	Hela-S3	cervix:	n/a	n/a
4	ZNF384	chr3:42641054-42643109	K562	blood:	n/a	n/a
5	POLR2A	chr3:42641221-42641244	HepG2	liver:	n/a	n/a
6	E2F4	chr3:42641136-42642309	MCF10A-Er-Src	breast:	n/a	chr3:42641918-42641927
7	POLR2A	chr3:42641234-42642911	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr3:42641201-42642954	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42629943..42634676-chr3:42635408..42643782,10	MCF-7	breast:
2	chr3:42640361..42643591-chr3:42693270..42696162,5	K562	blood:
3	chr3:42604560..42606277-chr3:42641170..42643967,2	K562	blood:
4	chr3:42640678..42643591-chr3:42694568..42696079,2	K562	blood:
5	chr3:42621283..42625330-chr3:42639303..42643596,7	MCF-7	breast:
6	chr3:42622208..42623993-chr3:42640628..42642693,2	MCF-7	breast:
7	chr3:42639395..42643636-chr3:42699754..42702498,4	K562	blood:

Variant related genes	Relation type
NKTR	TF binding region
ENSG00000114853	Chromatin interaction
ENSG00000230084	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000008324	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1062051	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13072295	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13085695	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13089845	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13090902	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13093680	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13095447	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17074602	0.81[ASN][1000 genomes]
rs17074662	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17074664	0.90[ASN][1000 genomes]
rs17074669	0.90[ASN][1000 genomes]
rs17074673	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17074674	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17074680	0.90[ASN][1000 genomes]
rs17074693	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241542	0.81[ASN][1000 genomes]
rs2271182	0.82[ASN][1000 genomes]
rs2284303	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2284304	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2300057	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2300058	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2302352	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33969824	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33984028	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34683820	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34687113	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34762478	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34801786	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34852409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34977988	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35216140	0.81[EUR][1000 genomes]
rs35506005	0.82[ASN][1000 genomes]
rs35676838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35770315	0.90[ASN][1000 genomes]
rs35871059	0.81[EUR][1000 genomes]
rs35890296	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36033201	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36043081	0.81[EUR][1000 genomes]
rs3774401	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3774402	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3774404	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3774406	0.82[ASN][1000 genomes]
rs3774407	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3821836	0.90[ASN][1000 genomes]
rs3846058	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3846059	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3856737	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3886782	0.95[ASN][1000 genomes]
rs56047094	0.81[EUR][1000 genomes]
rs56797870	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57259216	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58868911	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59914338	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60232916	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60348477	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60535002	0.81[EUR][1000 genomes]
rs61149998	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441928	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67059259	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67165547	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67533173	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67583158	0.81[EUR][1000 genomes]
rs6771105	0.81[EUR][1000 genomes]
rs6772312	0.94[ASN][1000 genomes]
rs6778982	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6782164	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67832425	0.81[EUR][1000 genomes]
rs6788548	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6793186	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6795296	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6797491	0.81[EUR][1000 genomes]
rs68004576	0.81[EUR][1000 genomes]
rs68028490	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68071013	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72864072	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73829255	0.81[EUR][1000 genomes]
rs7617403	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7617736	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7624628	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3415147	chr3:42638848-42641746	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	esv3404290	chr3:42638948-42643146	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42633200-42641400	Weak transcription	Aorta	Aorta
2	chr3:42633200-42641600	Weak transcription	Gastric	stomach
3	chr3:42633400-42641400	Weak transcription	Ovary	ovary
4	chr3:42633400-42641400	Weak transcription	Psoas Muscle	Psoas
5	chr3:42633400-42641400	Weak transcription	Right Ventricle	heart
6	chr3:42633400-42641600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:42633400-42641600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:42633400-42641600	Weak transcription	Esophagus	oesophagus
9	chr3:42633400-42641600	Weak transcription	Spleen	Spleen
10	chr3:42633600-42641400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:42633600-42641400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:42633600-42641400	Weak transcription	Brain Anterior Caudate	brain
13	chr3:42633600-42641600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:42633600-42641600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:42633600-42641600	Weak transcription	Pancreas	Pancrea
16	chr3:42634000-42641600	Weak transcription	Lung	lung
17	chr3:42635600-42641400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:42635600-42641600	Weak transcription	Small Intestine	intestine
19	chr3:42636000-42641400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:42636400-42641400	Weak transcription	Thymus	Thymus
21	chr3:42636800-42641400	Weak transcription	Left Ventricle	heart
22	chr3:42637000-42641400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:42638200-42641600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:42638600-42641400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:42640800-42643600	Active TSS	Hela-S3	cervix
26	chr3:42640800-42643800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:42641000-42641400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:42641000-42641400	Enhancers	Primary T cells fromperipheralblood	blood
29	chr3:42641000-42642200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:42641000-42643400	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr3:42641000-42643600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:42641200-42641400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:42641200-42641400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:42641200-42641400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:42641200-42641400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr3:42641200-42641400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:42641200-42641400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:42641200-42641400	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr3:42641200-42641400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr3:42641200-42641400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr3:42641200-42641400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:42641200-42641400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:42641200-42641400	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr3:42641200-42641400	Enhancers	Colon Smooth Muscle	Colon
45	chr3:42641200-42641400	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr3:42641200-42641400	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr3:42641200-42641400	Flanking Active TSS	GM12878-XiMat	blood
48	chr3:42641200-42641400	Active TSS	HepG2	liver
49	chr3:42641200-42641400	Enhancers	HSMM	muscle
50	chr3:42641200-42641400	Flanking Active TSS	HUVEC	blood vessel

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