Variant report

Variant	rs6741290
Chromosome Location	chr2:10264709-10264710
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:131)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:131 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:10264680-10264830	GM12864	blood:	n/a	n/a
2	RAD21	chr2:10264624-10265076	HepG2	liver:	n/a	n/a
3	SMC3	chr2:10264470-10265620	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr2:10264642-10265567	U87	brain:	n/a	n/a
5	RAD21	chr2:10264598-10265098	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr2:10264667-10264914	A549	lung:	n/a	n/a
7	POLR2A	chr2:10264636-10265562	U87	brain:	n/a	n/a
8	TEAD4	chr2:10264644-10265517	K562	blood:	n/a	n/a
9	RAD21	chr2:10264700-10265049	MCF-7	breast:	n/a	n/a
10	ARID3A	chr2:10264643-10264988	HepG2	liver:	n/a	n/a
11	CTCF	chr2:10264680-10264830	GM12868	blood:	n/a	n/a
12	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
13	CTCF	chr2:10264595-10265165	HCT-116	colon:	n/a	n/a
14	CTCF	chr2:10264700-10264850	HMEC	breast:	n/a	n/a
15	FOXA1	chr2:10264635-10265178	HepG2	liver:	n/a	n/a
16	MXI1	chr2:10261646-10264915	IMR90	lung:	n/a	n/a
17	RAD21	chr2:10264536-10265219	A549	lung:	n/a	n/a
18	CTCF	chr2:10264700-10264850	K562	blood:	n/a	n/a
19	CTCF	chr2:10264700-10264850	WERI-Rb-1	eye:	n/a	n/a
20	CTCF	chr2:10264700-10264850	HMF	breast:	n/a	n/a
21	CTCF	chr2:10264700-10264850	HEEpiC	esophagus:	n/a	n/a
22	POLR2A	chr2:10260062-10270747	GM19099	blood:	n/a	n/a
23	POLR2A	chr2:10260138-10270672	GM12878	blood:	n/a	n/a
24	CTCF	chr2:10264700-10264850	GM12865	blood:	n/a	n/a
25	SMC3	chr2:10264647-10265079	Hela-S3	cervix:	n/a	n/a
26	RAD21	chr2:10264604-10265115	A549	lung:	n/a	n/a
27	CTCF	chr2:10264660-10264810	WI-38	lung:	n/a	n/a
28	POLR2A	chr2:10260136-10264925	GM18951	blood:	n/a	n/a
29	CTCF	chr2:10264700-10264850	HAc	cerebellar:	n/a	n/a
30	CTCF	chr2:10264645-10265005	K562	blood:	n/a	n/a
31	RAD21	chr2:10264641-10264938	GM12878	blood:	n/a	n/a
32	FOXA1	chr2:10264667-10265147	HepG2	liver:	n/a	n/a
33	SIN3AK20	chr2:10264682-10264926	K562	blood:	n/a	n/a
34	CTCF	chr2:10263913-10265542	A549	lung:	n/a	n/a
35	BCLAF1	chr2:10264529-10267199	K562	blood:	n/a	n/a
36	CTCF	chr2:10264704-10264940	K562	blood:	n/a	n/a
37	POLR2A	chr2:10260053-10270807	PBDE	blood:	n/a	n/a
38	CTCF	chr2:10264591-10265035	K562	blood:	n/a	n/a
39	POLR2A	chr2:10264631-10265208	GM12892	blood:	n/a	n/a
40	CTCF	chr2:10264680-10264830	HBMEC	blood vessel:	n/a	n/a
41	CTCF	chr2:10264680-10264830	GM12866	blood:	n/a	n/a
42	RAD21	chr2:10264552-10265104	MCF-7	breast:	n/a	n/a
43	FOXA1	chr2:10264707-10265000	T-47D	breast:	n/a	n/a
44	TCF7L2	chr2:10264662-10264974	PANC-1	pancreas:	n/a	chr2:10264696-10264710 chr2:10264821-10264830
45	RAD21	chr2:10264703-10265067	ECC-1	luminal epithelium:	n/a	n/a
46	CTCF	chr2:10264700-10264850	BJ	skin:	n/a	n/a
47	SIN3A	chr2:10264669-10265028	GM12878	blood:	n/a	n/a
48	CTCF	chr2:10264612-10265104	MCF-7	breast:	n/a	n/a
49	RCOR1	chr2:10264655-10264989	K562	blood:	n/a	n/a
50	FOXM1	chr2:10264616-10265025	GM12878	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:10239900..10242865-chr2:10264207..10266171,2	K562	blood:
2	chr2:10215595..10217272-chr2:10263432..10266266,3	K562	blood:
3	chr2:10264613..10265297-chr2:10575160..10575706,2	MCF-7	breast:
4	chr2:10264086..10264925-chr2:10808106..10808865,2	MCF-7	breast:
5	chr2:10259653..10265917-chr2:10585320..10590295,8	MCF-7	breast:
6	chr2:10259839..10264771-chr2:10582056..10590038,19	K562	blood:
7	chr2:10181485..10190041-chr2:10258160..10265104,19	K562	blood:
8	chr2:10257984..10265070-chr2:10582045..10589780,17	K562	blood:
9	chr2:10261047..10264754-chr2:10441936..10445688,4	MCF-7	breast:
10	chr14:69618604..69621513-chr2:10263328..10265065,2	MCF-7	breast:
11	chr2:10262824..10265094-chr2:10557551..10560523,2	K562	blood:
12	chr2:10259710..10265084-chr2:10586364..10590442,7	MCF-7	breast:
13	chr2:10212808..10214371-chr2:10264025..10265652,2	MCF-7	breast:

No data

Variant related genes	Relation type
RRM2	TF binding region
ENSG00000115756	Chromatin interaction
ENSG00000139990	Chromatin interaction
ENSG00000115758	Chromatin interaction
ENSG00000206633	Chromatin interaction
ENSG00000172059	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	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs13392622	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2110643	0.96[ASN][1000 genomes]
rs34455011	0.85[ASN][1000 genomes]
rs4309551	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4668664	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs6432062	0.89[ASN][1000 genomes]
rs6432064	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6432065	0.96[ASN][1000 genomes]
rs6715884	0.96[ASN][1000 genomes]
rs6737932	0.95[ASN][1000 genomes]
rs6759180	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs717886	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs718215	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs729917	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7577887	0.97[ASN][1000 genomes]
rs7603436	0.95[ASN][1000 genomes]
rs7604817	0.92[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:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10260200-10265000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:10260600-10265200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:10260800-10264800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr2:10261800-10264800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr2:10262000-10265000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:10262400-10264800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:10262800-10264800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:10262800-10270400	Transcr. at gene 5' and 3'	Dnd41	blood
9	chr2:10263400-10264800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
10	chr2:10263400-10264800	Flanking Active TSS	NH-A	brain
11	chr2:10263400-10265000	Flanking Active TSS	HUVEC	blood vessel
12	chr2:10263400-10265400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:10263400-10267000	Weak transcription	Pancreas	Pancrea
14	chr2:10263600-10264800	Flanking Active TSS	Fetal Lung	lung
15	chr2:10263600-10265000	Flanking Active TSS	NHEK	skin
16	chr2:10263600-10265200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
17	chr2:10263600-10265200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:10263600-10265400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:10263600-10265400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
20	chr2:10263600-10265400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
21	chr2:10263600-10265400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
22	chr2:10263600-10265400	Transcr. at gene 5' and 3'	A549	lung
23	chr2:10263600-10265400	Transcr. at gene 5' and 3'	K562	blood
24	chr2:10263600-10266400	Weak transcription	Liver	Liver
25	chr2:10263800-10265200	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
26	chr2:10263800-10265400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:10263800-10266600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
28	chr2:10263800-10267000	Weak transcription	Right Atrium	heart
29	chr2:10263800-10272200	Weak transcription	Gastric	stomach
30	chr2:10263800-10277400	Weak transcription	Esophagus	oesophagus
31	chr2:10263800-10283600	Weak transcription	Spleen	Spleen
32	chr2:10264000-10264800	Active TSS	Fetal Intestine Large	intestine
33	chr2:10264000-10265000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:10264000-10265000	Active TSS	Fetal Kidney	kidney
35	chr2:10264000-10265000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:10264000-10265000	Active TSS	GM12878-XiMat	blood
37	chr2:10264000-10265000	Transcr. at gene 5' and 3'	HMEC	breast
38	chr2:10264000-10265000	Active TSS	HSMM	muscle
39	chr2:10264000-10265000	Weak transcription	HSMMtube	muscle
40	chr2:10264000-10265000	Active TSS	NHLF	lung
41	chr2:10264000-10265200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr2:10264000-10265200	Flanking Active TSS	HepG2	liver
43	chr2:10264000-10265400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:10264000-10265400	Active TSS	Fetal Brain Female	brain
45	chr2:10264000-10266000	Active TSS	Brain Germinal Matrix	brain
46	chr2:10264000-10266200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:10264000-10266600	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr2:10264000-10267400	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr2:10264200-10264800	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr2:10264200-10264800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood

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