Variant report

Variant	rs12713497
Chromosome Location	chr2:63926545-63926546
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	FOSL1	chr2:63925798-63926625	HCT-116	colon:	n/a	chr2:63926149-63926158 chr2:63926148-63926157
2	SPI1	chr2:63926447-63926740	GM12891	blood:	n/a	n/a
3	YY1	chr2:63926168-63926596	GM12878	blood:	n/a	n/a
4	SMC3	chr2:63926110-63926593	HepG2	liver:	n/a	chr2:63926369-63926383
5	RAD21	chr2:63926023-63926757	H1-hESC	embryonic stem cell:	n/a	chr2:63926368-63926387
6	RAD21	chr2:63926115-63926559	HepG2	liver:	n/a	chr2:63926368-63926387
7	CTCF	chr2:63926021-63926802	SK-N-SH	brain:	n/a	chr2:63926368-63926384 chr2:63926367-63926385 chr2:63926369-63926390
8	RAD21	chr2:63925948-63926772	HCT-116	colon:	n/a	chr2:63926368-63926387
9	CTCF	chr2:63926153-63926603	GM12878	blood:	n/a	chr2:63926368-63926384 chr2:63926367-63926385 chr2:63926369-63926390
10	RAD21	chr2:63926138-63926672	ECC-1	luminal epithelium:	n/a	chr2:63926368-63926387
11	JUND	chr2:63925798-63926977	Hela-S3	cervix:	n/a	chr2:63926149-63926158 chr2:63926788-63926799 chr2:63926148-63926157
12	RAD21	chr2:63926089-63926646	MCF-7	breast:	n/a	chr2:63926368-63926387
13	CBX3	chr2:63925864-63926673	HCT-116	colon:	n/a	n/a
14	RAD21	chr2:63926000-63926669	H1-hESC	embryonic stem cell:	n/a	chr2:63926368-63926387
15	JUND	chr2:63925851-63926872	H1-hESC	embryonic stem cell:	n/a	chr2:63926149-63926158 chr2:63926788-63926799 chr2:63926148-63926157
16	RAD21	chr2:63926113-63926552	ECC-1	luminal epithelium:	n/a	chr2:63926368-63926387
17	RAD21	chr2:63925963-63926820	A549	lung:	n/a	chr2:63926368-63926387
18	CTCF	chr2:63926143-63926583	H1-hESC	embryonic stem cell:	n/a	chr2:63926368-63926384 chr2:63926367-63926385 chr2:63926369-63926390
19	ARID3A	chr2:63926250-63926589	HepG2	liver:	n/a	n/a
20	SMC3	chr2:63925906-63926958	SK-N-SH	brain:	n/a	chr2:63926369-63926383
21	RAD21	chr2:63926211-63926652	GM12878	blood:	n/a	chr2:63926368-63926387
22	RAD21	chr2:63926165-63926578	SK-N-SH_RA	brain:	n/a	chr2:63926368-63926387
23	STAT3	chr2:63925368-63926565	MCF10A-Er-Src	breast:	n/a	chr2:63926148-63926157 chr2:63925808-63925816
24	FOS	chr2:63925523-63926968	MCF10A-Er-Src	breast:	n/a	chr2:63926149-63926158 chr2:63926147-63926158 chr2:63926148-63926157
25	POLR2A	chr2:63926000-63926605	MCF10A-Er-Src	breast:	n/a	n/a
26	CEBPB	chr2:63925734-63926551	Hela-S3	cervix:	n/a	n/a
27	CEBPB	chr2:63925528-63926574	A549	lung:	n/a	n/a
28	CTCF	chr2:63926540-63926690	HepG2	liver:	n/a	n/a
29	USF2	chr2:63925952-63926708	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr2:63926193-63926560	A549	lung:	n/a	chr2:63926368-63926384 chr2:63926367-63926385 chr2:63926369-63926390
31	CTCF	chr2:63926177-63926580	IMR90	lung:	n/a	chr2:63926368-63926384 chr2:63926367-63926385 chr2:63926369-63926390
32	SIN3A	chr2:63926095-63926556	H1-hESC	embryonic stem cell:	n/a	n/a
33	RAD21	chr2:63925881-63926847	Hela-S3	cervix:	n/a	chr2:63926368-63926387
34	FOSL2	chr2:63925755-63926967	A549	lung:	n/a	chr2:63926149-63926158 chr2:63926148-63926157
35	CTCF	chr2:63925247-63927001	A549	lung:	n/a	chr2:63926368-63926384 chr2:63926367-63926385 chr2:63926369-63926390
36	KAP1	chr2:63926009-63926557	U2OS	brain:	n/a	chr2:63926150-63926159
37	CTCF	chr2:63926088-63926647	MCF-7	breast:	n/a	chr2:63926368-63926384 chr2:63926367-63926385 chr2:63926369-63926390
38	EP300	chr2:63925888-63926838	Hela-S3	cervix:	n/a	chr2:63926149-63926158
39	RAD21	chr2:63926005-63926614	A549	lung:	n/a	chr2:63926368-63926387
40	POLR2A	chr2:63925728-63926549	U87	brain:	n/a	n/a
41	SMC3	chr2:63926079-63926600	GM12878	blood:	n/a	chr2:63926369-63926383
42	FOS	chr2:63925938-63927160	MCF10A-Er-Src	breast:	n/a	chr2:63926149-63926158 chr2:63926147-63926158 chr2:63926148-63926157
43	RAD21	chr2:63925969-63926570	SK-N-SH_RA	brain:	n/a	chr2:63926368-63926387
44	STAT3	chr2:63925434-63926801	MCF10A-Er-Src	breast:	n/a	chr2:63926148-63926157 chr2:63925808-63925816
45	CTCF	chr2:63926177-63926574	K562	blood:	n/a	chr2:63926368-63926384 chr2:63926367-63926385 chr2:63926369-63926390
46	RAD21	chr2:63925980-63926688	HepG2	liver:	n/a	chr2:63926368-63926387
47	CTCF	chr2:63926012-63926800	HCT-116	colon:	n/a	chr2:63926368-63926384 chr2:63926367-63926385 chr2:63926369-63926390
48	POLR2A	chr2:63925755-63926614	HUVEC	blood vessel:	n/a	n/a
49	RAD21	chr2:63926082-63926679	HepG2	liver:	n/a	chr2:63926368-63926387
50	YY1	chr2:63926154-63926550	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:63925946..63926752-chr2:64088066..64088909,2	MCF-7	breast:
2	chr2:63925442..63927694-chr2:64060712..64063478,2	MCF-7	breast:
3	chr2:63924196..63929131-chr2:64067029..64071463,7	MCF-7	breast:
4	chr2:63918680..63921430-chr2:63924139..63927284,3	MCF-7	breast:
5	chr2:63925927..63926628-chr2:64088095..64088826,2	K562	blood:
6	chr2:63924568..63927226-chr2:64063446..64066245,2	MCF-7	breast:
7	chr2:63925757..63927573-chr2:63973128..63975135,2	MCF-7	breast:
8	chr2:63925940..63927919-chr2:64072699..64075285,2	MCF-7	breast:
9	chr2:63924948..63928256-chr2:64067153..64069660,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221085	TF binding region
ENSG00000169764	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10168461	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10200146	0.80[JPT][hapmap]
rs10201844	0.89[CHB][hapmap]
rs10211360	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12612549	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs13006124	0.84[CHB][hapmap]
rs13384707	0.89[CHB][hapmap]
rs17619717	0.84[CHB][hapmap]
rs2168274	0.92[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4072113	0.84[CHB][hapmap]
rs4671528	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6546025	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs6546026	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs6546038	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs6546039	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs6726257	0.83[CHB][hapmap]
rs6737855	0.89[CHB][hapmap]
rs6741298	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6741584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6747307	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7597935	0.84[CHB][hapmap]
rs9309356	0.89[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834242	chr2:63891249-64045617	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63923800-63927200	Enhancers	Liver	Liver
2	chr2:63925400-63926600	Enhancers	H1 Cell Line	embryonic stem cell
3	chr2:63925400-63926600	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr2:63925400-63926600	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr2:63925400-63926800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:63925400-63926800	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr2:63925400-63926800	Enhancers	NH-A	brain
8	chr2:63925400-63927000	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr2:63925400-63927200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:63925400-63927200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:63925400-63927200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr2:63925400-63927200	Enhancers	HMEC	breast
13	chr2:63925400-63927200	Enhancers	HUVEC	blood vessel
14	chr2:63925400-63927800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:63925600-63926600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:63925600-63926600	Enhancers	Psoas Muscle	Psoas
17	chr2:63925600-63926800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr2:63925600-63926800	Enhancers	Adipose Nuclei	Adipose
19	chr2:63925600-63926800	Enhancers	NHLF	lung
20	chr2:63925600-63927200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:63925600-63927200	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr2:63925800-63926600	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr2:63925800-63926600	Flanking Active TSS	Osteobl	bone
24	chr2:63925800-63926800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr2:63925800-63926800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr2:63925800-63927000	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr2:63925800-63927000	Flanking Active TSS	A549	lung
28	chr2:63925800-63927200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:63925800-63927200	Enhancers	HSMMtube	muscle
30	chr2:63926000-63926600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:63926000-63926600	Flanking Active TSS	HepG2	liver
32	chr2:63926000-63926800	Enhancers	Stomach Smooth Muscle	stomach
33	chr2:63926000-63927000	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr2:63926200-63926600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:63926200-63926600	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr2:63926200-63926800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr2:63926400-63926600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr2:63926400-63926600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr2:63926400-63926800	Enhancers	NHDF-Ad	bronchial
40	chr2:63926400-63927000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:63926400-63927000	Enhancers	Hela-S3	cervix
42	chr2:63926400-63927200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:63926400-63927200	Enhancers	HSMM	muscle
44	chr2:63926400-63927200	Enhancers	NHEK	skin
45	chr2:63926400-63927400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:63926400-63927600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:63926400-63935400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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