Variant report

Variant	rs7638049
Chromosome Location	chr3:47204518-47204519
allele	C/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	MYBL2	chr3:47204479-47205009	HepG2	liver:	n/a	n/a
2	BCLAF1	chr3:47204267-47205023	GM12878	blood:	n/a	chr3:47204624-47204633 chr3:47204976-47204989 chr3:47204781-47204794
3	YY1	chr3:47204498-47206409	GM12878	blood:	n/a	chr3:47205587-47205598 chr3:47205468-47205479 chr3:47205189-47205198 chr3:47205321-47205332 chr3:47205279-47205293 chr3:47205256-47205270 chr3:47204848-47204862 chr3:47205252-47205266 chr3:47205258-47205267 chr3:47205253-47205267 chr3:47205109-47205118
4	MAX	chr3:47204474-47206415	K562	blood:	n/a	chr3:47205889-47205899
5	MYC	chr3:47204469-47206552	K562	blood:	n/a	chr3:47205889-47205899
6	YY1	chr3:47204499-47205030	GM12892	blood:	n/a	chr3:47204848-47204862
7	MAX	chr3:47204399-47206611	HCT-116	colon:	n/a	chr3:47205889-47205899
8	REST	chr3:47204200-47206694	H1-neurons	neurons:	n/a	chr3:47205082-47205095
9	MYC	chr3:47204271-47205286	A549	lung:	n/a	n/a
10	CHD1	chr3:47204412-47206570	H1-hESC	embryonic stem cell:	n/a	chr3:47205244-47205254
11	MAZ	chr3:47204296-47206660	K562	blood:	n/a	chr3:47205889-47205899
12	POLR2A	chr3:47204234-47204895	GM12878	blood:	n/a	n/a
13	TBP	chr3:47204299-47206472	K562	blood:	n/a	n/a
14	TBL1XR1	chr3:47204325-47206538	GM12878	blood:	n/a	n/a
15	ZNF143	chr3:47204503-47204703	K562	blood:	n/a	n/a
16	MTA3	chr3:47204504-47205047	GM12878	blood:	n/a	n/a
17	SIN3A	chr3:47204091-47206719	H1-hESC	embryonic stem cell:	n/a	chr3:47205749-47205760 chr3:47206305-47206316 chr3:47205587-47205598
18	CUX1	chr3:47203962-47204769	K562	blood:	n/a	n/a
19	HCFC1	chr3:47204218-47206975	Hela-S3	cervix:	n/a	n/a
20	CHD1	chr3:47203409-47206971	IMR90	lung:	n/a	chr3:47205244-47205254
21	ELF1	chr3:47204389-47204971	MCF-7	breast:	n/a	chr3:47204892-47204904 chr3:47204724-47204735 chr3:47204724-47204735
22	RUNX3	chr3:47204276-47205442	GM12878	blood:	n/a	chr3:47204670-47204687
23	NFIC	chr3:47204429-47205069	GM12878	blood:	n/a	n/a
24	EP300	chr3:47204209-47204678	GM12878	blood:	n/a	n/a
25	MAX	chr3:47204510-47206559	HepG2	liver:	n/a	chr3:47205889-47205899
26	MAX	chr3:47204488-47206714	Hela-S3	cervix:	n/a	chr3:47205889-47205899
27	MAX	chr3:47204439-47206550	ECC-1	luminal epithelium:	n/a	chr3:47205889-47205899
28	MTA3	chr3:47204418-47205072	GM12878	blood:	n/a	n/a
29	CHD1	chr3:47203534-47206662	GM12878	blood:	n/a	chr3:47205244-47205254
30	USF2	chr3:47204406-47204745	Hela-S3	cervix:	n/a	n/a
31	BHLHE40	chr3:47204184-47204795	GM12878	blood:	n/a	n/a
32	MXI1	chr3:47204342-47205317	K562	blood:	n/a	n/a
33	MYC	chr3:47204323-47205164	MCF10A-Er-Src	breast:	n/a	n/a
34	YY1	chr3:47204425-47206243	SK-N-SH	brain:	n/a	chr3:47205587-47205598 chr3:47205468-47205479 chr3:47205189-47205198 chr3:47205321-47205332 chr3:47205279-47205293 chr3:47205256-47205270 chr3:47204848-47204862 chr3:47205252-47205266 chr3:47205258-47205267 chr3:47205253-47205267 chr3:47205109-47205118
35	STAT5A	chr3:47204493-47205124	GM12878	blood:	n/a	chr3:47204622-47204633 chr3:47204514-47204525
36	ZNF274	chr3:47204104-47204869	K562	blood:	n/a	n/a
37	ELF1	chr3:47204500-47205046	HepG2	liver:	n/a	chr3:47204892-47204904 chr3:47204724-47204735 chr3:47204984-47204996 chr3:47204724-47204735
38	EP300	chr3:47204495-47205195	ECC-1	luminal epithelium:	n/a	chr3:47204937-47204953 chr3:47204848-47204857
39	RUNX3	chr3:47204311-47206855	GM12878	blood:	n/a	chr3:47204670-47204687
40	CEBPB	chr3:47203859-47204881	Hela-S3	cervix:	n/a	chr3:47204687-47204700 chr3:47204051-47204062
41	EBF1	chr3:47204473-47204990	GM12878	blood:	n/a	chr3:47204612-47204623
42	POLR2A	chr3:47204360-47206262	HepG2	liver:	n/a	n/a
43	TAL1	chr3:47204327-47204551	K562	blood:	n/a	chr3:47204354-47204362
44	MAZ	chr3:47204383-47206885	IMR90	lung:	n/a	chr3:47205889-47205899
45	CEBPB	chr3:47203849-47204545	K562	blood:	n/a	chr3:47204051-47204062
46	MXI1	chr3:47204296-47204968	Hela-S3	cervix:	n/a	n/a
47	UBTF	chr3:47204252-47206727	K562	blood:	n/a	n/a
48	TAF1	chr3:47204508-47205077	GM12878	blood:	n/a	n/a
49	YY1	chr3:47204456-47205478	GM12878	blood:	n/a	chr3:47205189-47205198 chr3:47205321-47205332 chr3:47205279-47205293 chr3:47205256-47205270 chr3:47204848-47204862 chr3:47205252-47205266 chr3:47205258-47205267 chr3:47205253-47205267 chr3:47205109-47205118
50	PML	chr3:47204359-47205158	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47203222..47204974-chr3:47216567..47218199,2	K562	blood:
2	chr3:47204122..47207133-chr3:47321636..47325818,4	K562	blood:
3	chr3:47204211..47206785-chr3:47421682..47423744,2	K562	blood:
4	chr3:47203577..47205455-chr3:47421565..47423969,3	MCF-7	breast:

Variant related genes	Relation type
KIF9-AS1	TF binding region
ENSG00000088727	Chromatin interaction
ENSG00000114648	Chromatin interaction
ENSG00000076201	Chromatin interaction
ENSG00000260236	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12486248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12487863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12489851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs12490244	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12490251	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12492463	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12493011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs12493723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12495173	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12495438	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17079425	1.00[JPT][hapmap]
rs17079512	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17079543	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17079580	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2291721	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3733093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes]
rs3816531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3821879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs3933020	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4082156	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4627772	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4683318	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4683321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683323	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683328	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs58206566	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59601660	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60285825	0.81[EUR][1000 genomes]
rs7641068	0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv590210	chr3:47126543-47214122	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv590211	chr3:47189485-47256057	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv3801	chr3:47201530-47246438	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr3:47166000-47204600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:47197400-47204600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:47202400-47204800	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr3:47202600-47204600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:47203000-47204600	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr3:47203000-47204800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:47203000-47207600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:47203200-47205800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:47203200-47207400	Active TSS	GM12878-XiMat	blood
10	chr3:47203200-47207600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr3:47203400-47204600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:47203400-47204800	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr3:47203400-47207200	Active TSS	Ovary	ovary
14	chr3:47203600-47204600	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr3:47203600-47204600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:47203600-47204600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:47203600-47204600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr3:47203600-47204600	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr3:47203600-47204600	Transcr. at gene 5' and 3'	K562	blood
20	chr3:47203600-47205000	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr3:47203600-47205200	Active TSS	Right Atrium	heart
22	chr3:47203600-47206600	Active TSS	Right Ventricle	heart
23	chr3:47203600-47207200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:47203600-47207200	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr3:47203600-47207200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:47203600-47207200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:47203600-47207200	Active TSS	HSMMtube	muscle
28	chr3:47203800-47204600	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr3:47203800-47204600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr3:47203800-47204600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr3:47203800-47204600	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr3:47203800-47204600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr3:47203800-47204800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr3:47203800-47206000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:47203800-47206600	Active TSS	Brain Germinal Matrix	brain
36	chr3:47203800-47206600	Active TSS	Fetal Thymus	thymus
37	chr3:47203800-47207000	Active TSS	Psoas Muscle	Psoas
38	chr3:47203800-47207200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:47203800-47207200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:47203800-47207200	Active TSS	Fetal Intestine Large	intestine
41	chr3:47203800-47207200	Active TSS	Fetal Intestine Small	intestine
42	chr3:47203800-47207200	Active TSS	Stomach Smooth Muscle	stomach
43	chr3:47203800-47207600	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr3:47203800-47207600	Active TSS	H1 Cell Line	embryonic stem cell
45	chr3:47203800-47207600	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr3:47204000-47204600	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr3:47204000-47204600	Flanking Active TSS	Brain Substantia Nigra	brain
48	chr3:47204000-47204600	Flanking Active TSS	Fetal Brain Male	brain
49	chr3:47204000-47204600	Enhancers	Spleen	Spleen
50	chr3:47204000-47205400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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