Variant report

Variant	rs6432065
Chromosome Location	chr2:10264057-10264058
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	POLR2A	chr2:10263652-10264206	GM12891	blood:	n/a	n/a
2	POLR2A	chr2:10259419-10264186	PANC-1	pancreas:	n/a	n/a
3	TCF12	chr2:10263662-10264474	SK-N-SH	brain:	n/a	n/a
4	EP300	chr2:10263851-10264180	SK-N-SH_RA	brain:	n/a	n/a
5	POLR2A	chr2:10263717-10264215	HepG2	liver:	n/a	n/a
6	CEBPB	chr2:10263915-10264285	Hela-S3	cervix:	n/a	n/a
7	HEY1	chr2:10260091-10268046	K562	blood:	n/a	chr2:10262408-10262423 chr2:10262559-10262574 chr2:10262366-10262381 chr2:10260481-10260496 chr2:10262702-10262717 chr2:10262368-10262383 chr2:10262406-10262421 chr2:10260417-10260432
8	FOS	chr2:10263897-10264347	MCF10A-Er-Src	breast:	n/a	n/a
9	MAX	chr2:10263755-10264243	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr2:10263891-10264100	GM12891	blood:	n/a	n/a
11	MXI1	chr2:10261646-10264915	IMR90	lung:	n/a	n/a
12	E2F4	chr2:10260258-10264398	MCF10A-Er-Src	breast:	n/a	chr2:10263286-10263298 chr2:10263232-10263243 chr2:10263232-10263243 chr2:10262368-10262378 chr2:10262230-10262238 chr2:10260481-10260490 chr2:10263232-10263243 chr2:10263232-10263243 chr2:10263236-10263243 chr2:10263229-10263246 chr2:10263287-10263294 chr2:10262228-10262239 chr2:10262402-10262411 chr2:10262229-10262239 chr2:10263287-10263294 chr2:10262231-10262238 chr2:10263233-10263248 chr2:10260867-10260882 chr2:10263227-10263242 chr2:10263287-10263294 chr2:10262230-10262238 chr2:10263232-10263243 chr2:10263235-10263243 chr2:10262825-10262836
13	POLR2A	chr2:10259553-10264206	PANC-1	pancreas:	n/a	n/a
14	MYC	chr2:10263900-10264391	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr2:10260062-10270747	GM19099	blood:	n/a	n/a
16	POLR2A	chr2:10260138-10270672	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:10260131-10264448	GM12878	blood:	n/a	n/a
18	FOS	chr2:10263792-10264319	MCF10A-Er-Src	breast:	n/a	n/a
19	HEY1	chr2:10263919-10264191	K562	blood:	n/a	n/a
20	POLR2A	chr2:10263380-10264135	K562	blood:	n/a	n/a
21	CTCF	chr2:10264040-10264190	HPF	lung:	n/a	n/a
22	POLR2A	chr2:10260117-10264144	K562	blood:	n/a	n/a
23	POLR2A	chr2:10260145-10264061	GM18526	blood:	n/a	n/a
24	POLR2A	chr2:10260136-10264925	GM18951	blood:	n/a	n/a
25	STAT3	chr2:10263945-10264308	MCF10A-Er-Src	breast:	n/a	n/a
26	CTCF	chr2:10263913-10265542	A549	lung:	n/a	n/a
27	SIN3AK20	chr2:10263903-10264209	A549	lung:	n/a	n/a
28	RUNX3	chr2:10263922-10264386	GM12878	blood:	n/a	n/a
29	POLR2A	chr2:10260099-10264428	HL-60	blood:	n/a	n/a
30	POLR2A	chr2:10263587-10264465	GM12892	blood:	n/a	n/a
31	POLR2A	chr2:10260053-10270807	PBDE	blood:	n/a	n/a
32	TBP	chr2:10263912-10264236	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr2:10263751-10264254	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr2:10260034-10264290	Hela-S3	cervix:	n/a	n/a
35	FOS	chr2:10263765-10264382	MCF10A-Er-Src	breast:	n/a	n/a
36	MYC	chr2:10263938-10264283	NB4	blood:	n/a	n/a
37	POLR2A	chr2:10260115-10264192	K562	blood:	n/a	n/a
38	POLR2A	chr2:10263631-10264203	GM12892	blood:	n/a	n/a
39	MYC	chr2:10264017-10264217	K562	blood:	n/a	n/a
40	POLR2A	chr2:10263739-10264389	U87	brain:	n/a	n/a
41	POLR2A	chr2:10260119-10270949	K562	blood:	n/a	n/a
42	PBX3	chr2:10263755-10264297	SK-N-SH	brain:	n/a	n/a
43	STAT3	chr2:10263946-10264289	MCF10A-Er-Src	breast:	n/a	n/a
44	EP300	chr2:10263864-10264248	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr2:10260062-10264201	GM12878	blood:	n/a	n/a
46	BCL3	chr2:10263957-10264335	GM12878	blood:	n/a	n/a
47	POLR2A	chr2:10263821-10264255	GM12892	blood:	n/a	n/a
48	MXI1	chr2:10263818-10264235	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr2:10263484-10265639	SK-N-SH	brain:	n/a	n/a
50	RCOR1	chr2:10263760-10264416	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:10215595..10217272-chr2:10263432..10266266,3	K562	blood:
2	chr2:10262306..10264072-chr2:10830698..10832625,2	K562	blood:
3	chr2:10259653..10265917-chr2:10585320..10590295,8	MCF-7	breast:
4	chr2:10259839..10264771-chr2:10582056..10590038,19	K562	blood:
5	chr2:10217388..10221351-chr2:10260365..10264430,6	K562	blood:
6	chr2:10181485..10190041-chr2:10258160..10265104,19	K562	blood:
7	chr2:10257984..10265070-chr2:10582045..10589780,17	K562	blood:
8	chr2:10261047..10264754-chr2:10441936..10445688,4	MCF-7	breast:
9	chr14:69618604..69621513-chr2:10263328..10265065,2	MCF-7	breast:
10	chr2:10262824..10265094-chr2:10557551..10560523,2	K562	blood:
11	chr2:10259710..10265084-chr2:10586364..10590442,7	MCF-7	breast:
12	chr2:10212808..10214371-chr2:10264025..10265652,2	MCF-7	breast:

Variant related genes	Relation type
RRM2	TF binding region
ENSG00000243819	Chromatin interaction
ENSG00000139990	Chromatin interaction
ENSG00000172059	Chromatin interaction
ENSG00000115758	Chromatin interaction
ENSG00000206633	Chromatin interaction
ENSG00000115756	Chromatin interaction
ENSG00000205795	Chromatin interaction
ENSG00000257135	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1130609	0.98[ASN][1000 genomes]
rs13392622	0.97[ASN][1000 genomes]
rs2110643	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34455011	0.86[ASN][1000 genomes]
rs4309551	0.97[ASN][1000 genomes]
rs4668664	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6432062	0.93[ASN][1000 genomes]
rs6432064	0.98[ASN][1000 genomes]
rs6715884	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6737932	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6741290	0.96[ASN][1000 genomes]
rs6759180	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs717886	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs718215	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs729917	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7577887	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7603436	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7604817	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv1007965	chr2:10154960-10276125	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1014790	chr2:10156968-10274855	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv999019	chr2:10157762-10273232	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv873633	chr2:10175442-10266563	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
7	nsv1010706	chr2:10189219-10266995	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10260000-10264200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:10260200-10264200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:10260200-10264200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:10260200-10264400	Active TSS	H1 Cell Line	embryonic stem cell
5	chr2:10260200-10264400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr2:10260200-10264400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr2:10260200-10265000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:10260400-10264600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:10260600-10265200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:10260800-10264800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr2:10261800-10264200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:10261800-10264200	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr2:10261800-10264800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr2:10262000-10264200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:10262000-10264200	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr2:10262000-10265000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:10262400-10264800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:10262800-10264200	Flanking Active TSS	Placenta	Placenta
19	chr2:10262800-10264800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:10262800-10270400	Transcr. at gene 5' and 3'	Dnd41	blood
21	chr2:10263000-10264200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:10263000-10264200	Flanking Active TSS	Fetal Intestine Small	intestine
23	chr2:10263000-10264600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr2:10263000-10264600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:10263200-10264200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
26	chr2:10263200-10264200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
27	chr2:10263200-10264200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
28	chr2:10263200-10264400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:10263400-10264200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:10263400-10264200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:10263400-10264200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
32	chr2:10263400-10264600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:10263400-10264800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
34	chr2:10263400-10264800	Flanking Active TSS	NH-A	brain
35	chr2:10263400-10265000	Flanking Active TSS	HUVEC	blood vessel
36	chr2:10263400-10265400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:10263400-10267000	Weak transcription	Pancreas	Pancrea
38	chr2:10263600-10264200	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr2:10263600-10264200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
40	chr2:10263600-10264200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:10263600-10264200	Flanking Active TSS	Fetal Heart	heart
42	chr2:10263600-10264800	Flanking Active TSS	Fetal Lung	lung
43	chr2:10263600-10265000	Flanking Active TSS	NHEK	skin
44	chr2:10263600-10265200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
45	chr2:10263600-10265200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:10263600-10265400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:10263600-10265400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
48	chr2:10263600-10265400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
49	chr2:10263600-10265400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
50	chr2:10263600-10265400	Transcr. at gene 5' and 3'	A549	lung

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