Variant report

Variant	rs2305640
Chromosome Location	chr3:47051026-47051027
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:135)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:135 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr3:47050770-47052797	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:47050603-47051909	GM18526	blood:	n/a	n/a
3	BCL3	chr3:47050764-47051326	GM12878	blood:	n/a	n/a
4	YY1	chr3:47050806-47051587	GM12891	blood:	n/a	n/a
5	ELF1	chr3:47050670-47051431	GM12878	blood:	n/a	n/a
6	ZNF143	chr3:47050783-47051203	GM12878	blood:	n/a	n/a
7	BHLHE40	chr3:47050889-47051236	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:47050454-47051433	U87	brain:	n/a	n/a
9	ELK1	chr3:47050865-47051174	GM12878	blood:	n/a	n/a
10	YY1	chr3:47050929-47051360	SK-N-SH_RA	brain:	n/a	n/a
11	POLR2A	chr3:47050449-47052087	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:47050649-47051273	SK-N-SH	brain:	n/a	n/a
13	RUNX3	chr3:47050867-47051663	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:47050979-47051283	GM12891	blood:	n/a	n/a
15	POLR2A	chr3:47050678-47051481	GM19099	blood:	n/a	n/a
16	EBF1	chr3:47050797-47051162	GM12878	blood:	n/a	n/a
17	PML	chr3:47050763-47051404	GM12878	blood:	n/a	n/a
18	TAF1	chr3:47050877-47051190	GM12878	blood:	n/a	n/a
19	SIN3AK20	chr3:47050698-47051286	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr3:47050724-47052790	GM12878	blood:	n/a	n/a
21	RAD21	chr3:47050684-47051185	SK-N-SH_RA	brain:	n/a	n/a
22	YY1	chr3:47050799-47051389	GM12878	blood:	n/a	n/a
23	TBP	chr3:47050694-47051680	H1-hESC	embryonic stem cell:	n/a	n/a
24	USF2	chr3:47050804-47051162	GM12878	blood:	n/a	n/a
25	MXI1	chr3:47050931-47051349	GM12878	blood:	n/a	n/a
26	STAT1	chr3:47050805-47051102	GM12878	blood:	n/a	n/a
27	MAX	chr3:47050386-47051780	H1-hESC	embryonic stem cell:	n/a	n/a
28	RCOR1	chr3:47050967-47051166	GM12878	blood:	n/a	n/a
29	PBX3	chr3:47050637-47051309	SK-N-SH	brain:	n/a	n/a
30	CTCF	chr3:47051000-47051150	HCPEpiC	choroid plexus:	n/a	n/a
31	POLR2A	chr3:47050631-47052806	GM12891	blood:	n/a	n/a
32	POLR2A	chr3:47050884-47051679	H1-hESC	embryonic stem cell:	n/a	n/a
33	GABPA	chr3:47050765-47051128	GM12878	blood:	n/a	n/a
34	EP300	chr3:47050995-47051181	GM12878	blood:	n/a	n/a
35	GTF2F1	chr3:47050887-47051137	H1-hESC	embryonic stem cell:	n/a	n/a
36	REST	chr3:47050850-47051150	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr3:47050917-47053219	K562	blood:	n/a	n/a
38	POLR2A	chr3:47050649-47052230	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:47050455-47052000	GM19193	blood:	n/a	n/a
40	EGR1	chr3:47050614-47051066	H1-hESC	embryonic stem cell:	n/a	chr3:47050623-47050636 chr3:47050626-47050635
41	MAX	chr3:47050509-47051353	SK-N-SH	brain:	n/a	n/a
42	RUNX3	chr3:47050808-47051785	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:47050781-47051508	GM12878	blood:	n/a	n/a
44	NFYB	chr3:47050740-47051198	GM12878	blood:	n/a	n/a
45	ELF1	chr3:47050683-47051981	GM12878	blood:	n/a	n/a
46	POU2F2	chr3:47050626-47051691	GM12878	blood:	n/a	chr3:47051615-47051627
47	GABPA	chr3:47050670-47051311	SK-N-SH	brain:	n/a	n/a
48	EBF1	chr3:47050787-47051096	GM12878	blood:	n/a	n/a
49	TAF7	chr3:47050665-47051519	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr3:47050610-47053359	GM12892	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47047312..47050228-chr3:47050509..47055807,4	MCF-7	breast:
2	chr17:41464193..41465701-chr3:47050147..47051667,2	K562	blood:
3	chr3:47038738..47041744-chr3:47049789..47052323,3	MCF-7	breast:
4	chr11:62607697..62610640-chr3:47050167..47053167,3	K562	blood:
5	chr3:47039779..47040407-chr3:47050513..47051136,2	MCF-7	breast:
6	chr3:47046288..47049439-chr3:47049485..47051071,3	MCF-7	breast:

No data

Variant related genes	Relation type
NRADDP	TF binding region
ENSG00000188825	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12485582	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12486248	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12489851	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491419	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12497141	0.82[ASN][1000 genomes]
rs17079425	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305632	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35201996	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3816531	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683276	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60285825	0.84[AMR][1000 genomes]
rs61364027	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7372834	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv876757	chr3:47018214-47058057	Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47031000-47053000	Strong transcription	Dnd41	blood
2	chr3:47039800-47058000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:47040600-47051400	Weak transcription	Fetal Heart	heart
4	chr3:47042200-47053000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:47043800-47057800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:47045000-47057600	Weak transcription	HepG2	liver
7	chr3:47048600-47055800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:47049000-47055000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:47049000-47055400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:47049800-47051400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:47049800-47051600	Genic enhancers	Primary monocytes fromperipheralblood	blood
12	chr3:47049800-47058200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:47050000-47051200	Genic enhancers	Spleen	Spleen
14	chr3:47050000-47051400	Active TSS	Brain Germinal Matrix	brain
15	chr3:47050000-47052000	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr3:47050200-47051400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:47050200-47051600	Active TSS	H1 Cell Line	embryonic stem cell
18	chr3:47050200-47051600	Active TSS	Brain Angular Gyrus	brain
19	chr3:47050200-47051800	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr3:47050200-47052000	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr3:47050200-47052200	Enhancers	Fetal Brain Male	brain
22	chr3:47050200-47058200	Weak transcription	Hela-S3	cervix
23	chr3:47050200-47059000	Weak transcription	A549	lung
24	chr3:47050200-47063800	Weak transcription	Stomach Mucosa	stomach
25	chr3:47050400-47051200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:47050400-47051200	Active TSS	Muscle Satellite Cultured Cells	--
27	chr3:47050400-47051200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:47050400-47051200	Active TSS	Colonic Mucosa	Colon
29	chr3:47050400-47051200	Active TSS	HSMM	muscle
30	chr3:47050400-47051200	Active TSS	NHLF	lung
31	chr3:47050400-47051400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:47050400-47051400	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:47050400-47051400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:47050400-47051400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:47050400-47051400	Active TSS	Fetal Brain Female	brain
36	chr3:47050400-47051400	Active TSS	GM12878-XiMat	blood
37	chr3:47050400-47051400	Active TSS	Osteobl	bone
38	chr3:47050400-47051600	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr3:47050400-47051600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:47050400-47051600	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr3:47050400-47051600	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr3:47050400-47051600	Active TSS	Duodenum Mucosa	Duodenum
43	chr3:47050400-47051600	Active TSS	Fetal Kidney	kidney
44	chr3:47050400-47051600	Active TSS	Psoas Muscle	Psoas
45	chr3:47050400-47051600	Active TSS	Rectal Smooth Muscle	rectum
46	chr3:47050400-47051800	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr3:47050400-47051800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:47050400-47051800	Active TSS	Brain Anterior Caudate	brain
49	chr3:47050400-47051800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr3:47050400-47052000	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived

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