Variant report

Variant	rs7712260
Chromosome Location	chr5:90515524-90515525
allele	C/G
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	RFX5	chr5:90514784-90515825	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr5:90515397-90516122	SK-N-SH	brain:	n/a	chr5:90516084-90516093 chr5:90515785-90515803 chr5:90515787-90515808 chr5:90515788-90515801
3	FOXM1	chr5:90514627-90515720	MCF-7	breast:	n/a	n/a
4	CEBPB	chr5:90514705-90515745	A549	lung:	n/a	chr5:90515127-90515138 chr5:90515181-90515189
5	BRCA1	chr5:90514682-90515579	Hela-S3	cervix:	n/a	n/a
6	JUND	chr5:90514855-90515703	Hela-S3	cervix:	n/a	n/a
7	FOXA2	chr5:90514665-90515616	A549	lung:	n/a	chr5:90515313-90515325
8	RAD21	chr5:90514980-90515985	IMR90	lung:	n/a	chr5:90515791-90515803 chr5:90515957-90515967 chr5:90515786-90515805
9	CEBPB	chr5:90514706-90515549	Hela-S3	cervix:	n/a	chr5:90515127-90515138 chr5:90515181-90515189
10	GATA3	chr5:90514503-90515684	MCF-7	breast:	n/a	chr5:90514798-90514814 chr5:90514866-90514875 chr5:90514802-90514811
11	MYC	chr5:90514887-90515598	Hela-S3	cervix:	n/a	n/a
12	MAX	chr5:90514832-90515892	NB4	blood:	n/a	n/a
13	NR2F2	chr5:90514698-90515636	MCF-7	breast:	n/a	n/a
14	TCF7L2	chr5:90514804-90515583	Hela-S3	cervix:	n/a	chr5:90515461-90515475
15	CTCF	chr5:90515511-90516033	MCF-7	breast:	n/a	chr5:90515785-90515803 chr5:90515787-90515808 chr5:90515788-90515801
16	RAD21	chr5:90515247-90516047	MCF-7	breast:	n/a	chr5:90515791-90515803 chr5:90515957-90515967 chr5:90515786-90515805
17	SIN3AK20	chr5:90514486-90515867	MCF-7	breast:	n/a	n/a
18	SIN3AK20	chr5:90514717-90515620	MCF-7	breast:	n/a	n/a
19	HDAC2	chr5:90514869-90515535	MCF-7	breast:	n/a	chr5:90515037-90515046 chr5:90515313-90515322
20	RAD21	chr5:90515393-90516079	A549	lung:	n/a	chr5:90515791-90515803 chr5:90515957-90515967 chr5:90515786-90515805
21	FOSL2	chr5:90514779-90515601	MCF-7	breast:	n/a	n/a
22	GATA3	chr5:90514596-90515638	A549	lung:	n/a	chr5:90514798-90514814 chr5:90514866-90514875 chr5:90514802-90514811
23	MAX	chr5:90514854-90515814	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr5:90515400-90515550	HRE	kidney:	n/a	n/a
25	TEAD4	chr5:90514864-90515601	A549	lung:	n/a	n/a
26	MAX	chr5:90514852-90515596	MCF-7	breast:	n/a	n/a
27	FOXM1	chr5:90514828-90515637	MCF-7	breast:	n/a	n/a
28	SMC3	chr5:90515415-90516233	SK-N-SH	brain:	n/a	chr5:90515957-90515967 chr5:90515787-90515801 chr5:90516080-90516094
29	SIX5	chr5:90514815-90515730	A549	lung:	n/a	n/a
30	FOSL2	chr5:90514598-90515813	A549	lung:	n/a	n/a
31	MAX	chr5:90514720-90515626	A549	lung:	n/a	n/a
32	CEBPB	chr5:90514755-90515603	MCF-7	breast:	n/a	chr5:90515127-90515138 chr5:90515181-90515189
33	EGR1	chr5:90515242-90515608	MCF-7	breast:	n/a	n/a
34	MAZ	chr5:90514976-90515551	Hela-S3	cervix:	n/a	n/a
35	USF2	chr5:90515043-90515872	Hela-S3	cervix:	n/a	n/a
36	RAD21	chr5:90515454-90516103	SK-N-SH	brain:	n/a	chr5:90515791-90515803 chr5:90515957-90515967 chr5:90515786-90515805
37	EP300	chr5:90514566-90515933	A549	lung:	n/a	chr5:90515312-90515322 chr5:90515036-90515046 chr5:90515909-90515919
38	GATA3	chr5:90514462-90515964	A549	lung:	n/a	chr5:90514798-90514814 chr5:90514866-90514875 chr5:90514802-90514811
39	RCOR1	chr5:90514799-90515563	Hela-S3	cervix:	n/a	n/a
40	NR2F2	chr5:90514666-90515637	MCF-7	breast:	n/a	n/a
41	MAX	chr5:90514970-90515757	A549	lung:	n/a	n/a
42	NR3C1	chr5:90514848-90515596	A549	lung:	n/a	n/a
43	FOXA2	chr5:90514743-90515730	A549	lung:	n/a	chr5:90515313-90515325
44	RAD21	chr5:90515154-90515947	A549	lung:	n/a	chr5:90515791-90515803 chr5:90515786-90515805
45	BCL3	chr5:90514787-90515605	A549	lung:	n/a	chr5:90514996-90515005
46	PRDM1	chr5:90514698-90515846	Hela-S3	cervix:	n/a	n/a
47	STAT1	chr5:90514798-90515960	Hela-S3	cervix:	n/a	chr5:90515497-90515505
48	SP1	chr5:90514629-90515773	A549	lung:	n/a	n/a
49	JUND	chr5:90514742-90515548	MCF-7	breast:	n/a	n/a
50	TCF7L2	chr5:90514782-90515614	MCF-7	breast:	n/a	chr5:90515461-90515475

No.	Distal block	Cell Line	Cell type
1	chr5:90457529..90462053-chr5:90513611..90518131,5	MCF-7	breast:
2	chr5:90513015..90523645-chr5:90674785..90682171,21	K562	blood:
3	chr5:90512455..90524285-chr5:90673793..90683360,52	MCF-7	breast:
4	chr5:90515297..90516283-chr5:90715097..90715818,3	K562	blood:
5	chr5:90398592..90401389-chr5:90514877..90517516,2	MCF-7	breast:
6	chr5:90514693..90517546-chr5:90521705..90523239,2	MCF-7	breast:
7	chr5:90514828..90516837-chr5:90519482..90521543,2	MCF-7	breast:
8	chr5:90510244..90526030-chr5:90672528..90682389,53	MCF-7	breast:
9	chr5:90512732..90524610-chr5:90674652..90682171,24	K562	blood:
10	chr5:90514930..90517107-chr5:90575291..90577972,2	MCF-7	breast:
11	chr5:90514822..90516620-chr5:90517523..90520846,3	MCF-7	breast:
12	chr5:90515350..90516235-chr5:90680436..90681312,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212930	TF binding region
ENSG00000234292	Chromatin interaction
ENSG00000251093	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000212930	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2048454	1.00[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs2973460	0.90[CEU][hapmap]
rs4916706	0.90[CEU][hapmap]
rs4916707	0.81[CEU][hapmap]
rs4916853	0.90[CEU][hapmap];0.92[TSI][hapmap]
rs4916857	0.90[CEU][hapmap];0.92[TSI][hapmap]
rs6865066	0.90[CEU][hapmap];0.92[TSI][hapmap]
rs6865269	0.84[TSI][hapmap]
rs73177675	0.85[EUR][1000 genomes]
rs7341005	0.90[CEU][hapmap]
rs7704529	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs7705128	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv508369	chr5:90487017-90518540	Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90514200-90515800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:90514200-90515800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:90514200-90516600	Enhancers	Hela-S3	cervix
4	chr5:90514200-90517200	Enhancers	Placenta Amnion	Placenta Amnion
5	chr5:90514400-90515600	Enhancers	Fetal Intestine Large	intestine
6	chr5:90514400-90515800	Enhancers	K562	blood
7	chr5:90514400-90515800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr5:90514400-90516000	Enhancers	Primary B cells from cord blood	blood
9	chr5:90514400-90516000	Enhancers	Adipose Nuclei	Adipose
10	chr5:90514400-90516200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:90514400-90516200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr5:90514600-90515600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:90514800-90515600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:90514800-90515600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr5:90514800-90515600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:90514800-90515600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr5:90514800-90515600	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr5:90514800-90515600	Flanking Active TSS	A549	lung
19	chr5:90514800-90515600	Enhancers	HMEC	breast
20	chr5:90514800-90515600	Enhancers	NHLF	lung
21	chr5:90514800-90515800	Enhancers	HSMMtube	muscle
22	chr5:90514800-90515800	Flanking Active TSS	Osteobl	bone
23	chr5:90514800-90516400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:90515000-90515600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:90515000-90515800	Enhancers	Stomach Mucosa	stomach
26	chr5:90515000-90515800	Enhancers	NHDF-Ad	bronchial
27	chr5:90515000-90516000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr5:90515000-90516000	Enhancers	HSMM	muscle
29	chr5:90515200-90515800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:90515200-90516000	Enhancers	Brain Hippocampus Middle	brain
31	chr5:90515200-90516200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:90515200-90516400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:90515200-90519200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:90515200-90519800	Enhancers	Placenta	Placenta
35	chr5:90515400-90516000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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