Variant report

Variant	rs10889120
Chromosome Location	chr1:59283572-59283573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr1:59283552-59284401	ECC-1	luminal epithelium:	n/a	n/a
2	TEAD4	chr1:59283567-59284366	SK-N-SH	brain:	n/a	chr1:59284139-59284148
3	NFIC	chr1:59283415-59284434	SK-N-SH	brain:	n/a	n/a
4	EP300	chr1:59283561-59284324	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr1:59283415-59284453	SK-N-SH	brain:	n/a	chr1:59283937-59283945
6	EP300	chr1:59283517-59284267	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr1:59283549-59284392	SK-N-SH	brain:	n/a	chr1:59283937-59283945
8	GATA3	chr1:59283530-59284423	SK-N-SH	brain:	n/a	n/a
9	EP300	chr1:59283555-59284379	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr1:59283535-59284241	ECC-1	luminal epithelium:	n/a	chr1:59283937-59283945

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:59279353..59283854-chr1:59287313..59291525,6	MCF-7	breast:
2	chr1:59245489..59255081-chr1:59277954..59283925,49	MCF-7	breast:
3	chr1:59280122..59283663-chr1:59349956..59353437,4	K562	blood:
4	chr1:59281044..59283680-chr1:59353136..59355336,2	K562	blood:
5	chr1:59243405..59253875-chr1:59275011..59289058,45	MCF-7	breast:
6	chr1:59243458..59255133-chr1:59272031..59283720,29	K562	blood:
7	chr1:59279921..59284497-chr1:59286325..59289409,4	K562	blood:
8	chr1:59280920..59283588-chr1:59288340..59291242,3	MCF-7	breast:
9	chr1:59280214..59283774-chr1:59346159..59349299,3	MCF-7	breast:
10	chr1:59279591..59281416-chr1:59282634..59284464,2	MCF-7	breast:
11	chr1:59283313..59285516-chr1:59290081..59292276,2	K562	blood:
12	chr1:59283326..59286068-chr1:59299643..59302569,3	K562	blood:
13	chr1:59271833..59274083-chr1:59283386..59285581,2	K562	blood:
14	chr1:59258641..59262017-chr1:59281438..59284393,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272226	TF binding region
ENSG00000177606	Chromatin interaction
ENSG00000234807	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1923943	1.00[AFR][1000 genomes]
rs2746080	1.00[MEX][hapmap]
rs2811892	1.00[MEX][hapmap]
rs522103	1.00[MEX][hapmap]
rs586509	1.00[MEX][hapmap]
rs6656813	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6675607	1.00[MEX][hapmap]
rs6703586	1.00[MEX][hapmap]
rs678283	1.00[MEX][hapmap]
rs7541519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59282400-59284200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:59282400-59284400	Enhancers	HSMM	muscle
3	chr1:59282400-59284600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:59282400-59284600	Enhancers	HMEC	breast
5	chr1:59282400-59285000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:59282400-59285000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:59282400-59285800	Enhancers	NHEK	skin
8	chr1:59282400-59286000	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:59282400-59286000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:59282400-59286000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:59282400-59287000	Weak transcription	Esophagus	oesophagus
12	chr1:59282400-59289200	Weak transcription	Placenta	Placenta
13	chr1:59282400-59289800	Weak transcription	Gastric	stomach
14	chr1:59282400-59290200	Weak transcription	Lung	lung
15	chr1:59282400-59290400	Weak transcription	Pancreas	Pancrea
16	chr1:59282400-59293800	Weak transcription	Aorta	Aorta
17	chr1:59282600-59283600	Weak transcription	Fetal Lung	lung
18	chr1:59282600-59284000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:59282600-59284000	Enhancers	Hela-S3	cervix
20	chr1:59282600-59285200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:59282600-59285800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:59282600-59285800	Enhancers	NH-A	brain
23	chr1:59282600-59285800	Enhancers	NHDF-Ad	bronchial
24	chr1:59282600-59285800	Enhancers	NHLF	lung
25	chr1:59282600-59285800	Enhancers	Osteobl	bone
26	chr1:59282600-59286000	Enhancers	HUVEC	blood vessel
27	chr1:59282600-59287000	Weak transcription	Left Ventricle	heart
28	chr1:59282600-59288800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:59282600-59290200	Weak transcription	Ovary	ovary
30	chr1:59282600-59290200	Weak transcription	Right Atrium	heart
31	chr1:59282600-59290200	Weak transcription	Right Ventricle	heart
32	chr1:59282800-59283600	Weak transcription	Fetal Stomach	stomach
33	chr1:59282800-59283600	Enhancers	A549	lung
34	chr1:59282800-59285000	Weak transcription	Fetal Intestine Small	intestine
35	chr1:59282800-59285200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:59282800-59285400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:59282800-59285400	Weak transcription	Fetal Intestine Large	intestine
38	chr1:59282800-59285800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:59282800-59285800	Weak transcription	Fetal Heart	heart
40	chr1:59282800-59288600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr1:59282800-59288800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:59282800-59289000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:59282800-59289600	Weak transcription	Small Intestine	intestine
44	chr1:59282800-59290200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:59283000-59284800	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr1:59283000-59285000	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr1:59283000-59285200	Weak transcription	HepG2	liver
48	chr1:59283000-59285400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr1:59283000-59285600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:59283000-59285600	Weak transcription	Duodenum Mucosa	Duodenum

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