Variant report

Variant	rs10486559
Chromosome Location	chr7:27784458-27784459
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	CTCF	chr7:27784442-27785107	K562	blood:	n/a	chr7:27784884-27784905
2	RAD21	chr7:27784445-27785235	HCT-116	colon:	n/a	chr7:27784596-27784608
3	FOXA2	chr7:27784278-27784476	HepG2	liver:	n/a	chr7:27784444-27784456
4	MXI1	chr7:27784054-27785269	SK-N-SH	brain:	n/a	n/a
5	SMC3	chr7:27784160-27785214	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr7:27784400-27784550	BJ	skin:	n/a	n/a
7	SP1	chr7:27784456-27785225	A549	lung:	n/a	n/a
8	CTCF	chr7:27784449-27785284	SK-N-SH	brain:	n/a	chr7:27784884-27784905
9	CTCF	chr7:27784392-27785235	HCT-116	colon:	n/a	chr7:27784884-27784905
10	CTCF	chr7:27784085-27785285	A549	lung:	n/a	chr7:27784884-27784905
11	FOXA1	chr7:27784260-27784507	HepG2	liver:	n/a	chr7:27784444-27784456
12	POLR2A	chr7:27784259-27785075	K562	blood:	n/a	n/a
13	EP300	chr7:27784316-27785045	K562	blood:	n/a	n/a
14	POLR2A	chr7:27784365-27785024	A549	lung:	n/a	n/a
15	MYC	chr7:27784451-27785037	MCF10A-Er-Src	breast:	n/a	n/a
16	TCF12	chr7:27784378-27785248	A549	lung:	n/a	n/a
17	FOXA2	chr7:27784166-27784703	A549	lung:	n/a	chr7:27784444-27784456
18	EP300	chr7:27784457-27785180	A549	lung:	n/a	n/a
19	ARID3A	chr7:27784310-27784503	K562	blood:	n/a	n/a
20	RAD21	chr7:27784300-27785292	SK-N-SH	brain:	n/a	chr7:27784596-27784608
21	FOXA1	chr7:27784162-27785102	HepG2	liver:	n/a	chr7:27784444-27784456
22	FOXA2	chr7:27784121-27784622	HepG2	liver:	n/a	chr7:27784444-27784456
23	CTCF	chr7:27784440-27784590	Caco-2	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:27699948..27706867-chr7:27775418..27784557,21	K562	blood:
2	chr7:27702844..27705316-chr7:27782990..27784557,2	K562	blood:
3	chr7:27777088..27781357-chr7:27783261..27787943,9	MCF-7	breast:
4	chr7:27783237..27786573-chr7:27802443..27806955,4	K562	blood:
5	chr7:27777249..27781364-chr7:27781538..27788730,11	MCF-7	breast:
6	chr7:27783427..27786063-chr7:27789814..27792025,2	MCF-7	breast:
7	chr7:27784235..27786861-chr7:27801505..27804201,3	K562	blood:

Variant related genes	Relation type
ENSG00000229893	TF binding region
ENSG00000106052	Chromatin interaction
ENSG00000229893	Chromatin interaction
ENSG00000106049	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10155851	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10225487	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10267854	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10277437	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10486549	0.91[CEU][hapmap]
rs10951184	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12666082	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12667470	0.95[CEU][hapmap]
rs16874364	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874393	0.82[CEU][hapmap]
rs16874395	0.82[CEU][hapmap]
rs17150563	0.86[EUR][1000 genomes]
rs17155498	0.95[CEU][hapmap]
rs17155505	0.95[CEU][hapmap]
rs17155537	0.91[CEU][hapmap]
rs17155702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17155943	0.81[EUR][1000 genomes]
rs17155950	0.86[CEU][hapmap]
rs2051830	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2074579	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2074769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2107413	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2108309	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2158388	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2192559	0.95[CEU][hapmap]
rs2237339	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237340	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2237341	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2285931	0.85[EUR][1000 genomes]
rs2299106	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2391450	0.87[CEU][hapmap]
rs2391488	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3779473	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3940270	0.85[CEU][hapmap]
rs4719907	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4719908	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4722741	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57932688	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58314651	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58857361	0.82[EUR][1000 genomes]
rs62449629	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62449639	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62449640	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62451077	0.81[EUR][1000 genomes]
rs62451079	0.80[EUR][1000 genomes]
rs62454806	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62454945	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6462048	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6462049	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6462052	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6462053	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6944251	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6944913	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6971813	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6972821	0.95[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72598505	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs759268	0.95[CEU][hapmap]
rs7784038	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7801301	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7803019	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7803227	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7809735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1028469	chr7:27767795-27939667	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3504587	chr7:27782321-27784475	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv2603706	chr7:27783015-27784618	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27780600-27784600	Weak transcription	Spleen	Spleen
2	chr7:27780800-27784600	Weak transcription	Left Ventricle	heart
3	chr7:27780800-27788800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:27780800-27789400	Weak transcription	Lung	lung
5	chr7:27780800-27796400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:27780800-27805600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:27780800-27810200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:27780800-27815200	Weak transcription	Gastric	stomach
9	chr7:27781000-27784600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:27781000-27784600	Weak transcription	Brain Substantia Nigra	brain
11	chr7:27781000-27784600	Weak transcription	Colonic Mucosa	Colon
12	chr7:27781000-27784600	Weak transcription	Ovary	ovary
13	chr7:27781000-27789000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr7:27781000-27800200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:27781000-27861800	Weak transcription	Aorta	Aorta
16	chr7:27781200-27784600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr7:27781200-27784600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr7:27781200-27784600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:27781200-27784600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr7:27781200-27784600	Weak transcription	Brain Anterior Caudate	brain
21	chr7:27781200-27784600	Weak transcription	Fetal Heart	heart
22	chr7:27781200-27784600	Weak transcription	Fetal Kidney	kidney
23	chr7:27781200-27784600	Weak transcription	Fetal Lung	lung
24	chr7:27781200-27784600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr7:27781200-27784600	Weak transcription	HMEC	breast
26	chr7:27781200-27784600	Weak transcription	HSMM	muscle
27	chr7:27781200-27784600	Weak transcription	NHEK	skin
28	chr7:27781200-27788000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr7:27781200-27788000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr7:27781200-27788400	Weak transcription	Brain Hippocampus Middle	brain
31	chr7:27781200-27788800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr7:27781200-27789000	Weak transcription	Fetal Thymus	thymus
33	chr7:27781200-27789400	Weak transcription	Thymus	Thymus
34	chr7:27781200-27789600	Weak transcription	Fetal Brain Female	brain
35	chr7:27781200-27790200	Weak transcription	Fetal Brain Male	brain
36	chr7:27781200-27791800	Weak transcription	Right Ventricle	heart
37	chr7:27781200-27792000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr7:27781400-27784600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr7:27781400-27784600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:27781400-27784600	Weak transcription	Brain Angular Gyrus	brain
41	chr7:27781400-27784600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr7:27781400-27784600	Weak transcription	Psoas Muscle	Psoas
43	chr7:27781400-27784800	Weak transcription	Right Atrium	heart
44	chr7:27781400-27789400	Weak transcription	Fetal Muscle Leg	muscle
45	chr7:27781400-27789600	Weak transcription	Esophagus	oesophagus
46	chr7:27781400-27799600	Weak transcription	Fetal Stomach	stomach
47	chr7:27781400-27803200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr7:27781400-27812800	Weak transcription	Brain Germinal Matrix	brain
49	chr7:27781600-27784600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr7:27782000-27784600	Weak transcription	Brain Cingulate Gyrus	brain

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