Variant report

Variant	rs56020062
Chromosome Location	chr9:103200713-103200714
allele	A/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	RAD21	chr9:103199961-103200722	SK-N-SH	brain:	n/a	chr9:103200332-103200341 chr9:103200327-103200341 chr9:103200323-103200342
2	CTCF	chr9:103200620-103200770	AG04450	lung:	n/a	n/a
3	CTCF	chr9:103199903-103200771	A549	lung:	n/a	chr9:103200320-103200341 chr9:103200327-103200340 chr9:103200326-103200342 chr9:103200325-103200343 chr9:103200332-103200339

No.	Distal block	Cell Line	Cell type
1	chr9:103197970..103201753-chr9:103212860..103216897,4	K562	blood:
2	chr9:103200219..103201742-chr9:103202494..103205491,2	MCF-7	breast:
3	chr9:103198603..103202424-chr9:103204469..103207359,3	K562	blood:
4	chr9:103199462..103202264-chr9:103213712..103215287,2	MCF-7	breast:
5	chr9:103189181..103190066-chr9:103200242..103200789,3	MCF-7	breast:
6	chr9:103199955..103200924-chr9:103231541..103232083,2	K562	blood:

Variant related genes	Relation type
MSANTD3	TF binding region
TMEFF1	TF binding region
MSANTD3-TMEFF1	TF binding region
ENSG00000251349	Chromatin interaction
ENSG00000066697	Chromatin interaction
ENSG00000241697	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10465118	1.00[EUR][1000 genomes]
rs10465119	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10465145	0.85[EUR][1000 genomes]
rs10512270	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10512271	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10819775	0.90[EUR][1000 genomes]
rs10819776	0.83[ASN][1000 genomes]
rs10819779	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10819781	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10819782	0.83[ASN][1000 genomes]
rs10989085	0.90[EUR][1000 genomes]
rs10989090	0.83[ASN][1000 genomes]
rs10989091	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10989092	0.83[ASN][1000 genomes]
rs10989094	0.83[ASN][1000 genomes]
rs10989095	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10989097	0.83[ASN][1000 genomes]
rs10989099	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10989103	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989107	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989108	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989111	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989113	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989114	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989115	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989124	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989131	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989134	0.91[AMR][1000 genomes]
rs10989140	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989142	0.90[AMR][1000 genomes]
rs10989144	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989145	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989147	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989150	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989151	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989154	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12004257	0.82[ASN][1000 genomes]
rs12056981	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12236071	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12236952	0.95[EUR][1000 genomes]
rs12237166	0.83[ASN][1000 genomes]
rs12237481	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12238560	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12682741	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12683122	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12683548	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12684454	0.83[ASN][1000 genomes]
rs16919136	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16919174	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1930245	0.83[ASN][1000 genomes]
rs1930246	0.83[ASN][1000 genomes]
rs2274881	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55827987	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56012200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56050588	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56122790	0.86[EUR][1000 genomes]
rs56163523	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56170030	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59611728	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7024666	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7034154	0.83[ASN][1000 genomes]
rs7041933	0.83[ASN][1000 genomes]
rs7046659	0.83[ASN][1000 genomes]
rs72735107	0.90[EUR][1000 genomes]
rs72735119	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72735122	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72735140	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72735148	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72735154	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7869933	0.83[ASN][1000 genomes]

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	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv825012	chr9:103152205-103256281	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv614955	chr9:103181596-103261227	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103190400-103206000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:103190400-103214200	Weak transcription	Thymus	Thymus
3	chr9:103190600-103214400	Weak transcription	Primary B cells from cord blood	blood
4	chr9:103190600-103224600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:103190800-103204000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:103190800-103204400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr9:103190800-103206000	Weak transcription	Primary T cells from cord blood	blood
8	chr9:103190800-103206800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr9:103190800-103207200	Weak transcription	Fetal Lung	lung
10	chr9:103190800-103213200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr9:103190800-103217600	Weak transcription	Fetal Intestine Large	intestine
12	chr9:103191000-103203400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:103191000-103206600	Weak transcription	Colonic Mucosa	Colon
14	chr9:103191200-103204200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr9:103191200-103214200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr9:103191600-103201200	Weak transcription	Fetal Muscle Leg	muscle
17	chr9:103191600-103202000	Weak transcription	Placenta	Placenta
18	chr9:103191600-103202400	Weak transcription	Small Intestine	intestine
19	chr9:103191600-103204200	Weak transcription	Ovary	ovary
20	chr9:103191600-103204400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr9:103191600-103204400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr9:103191600-103204400	Weak transcription	Gastric	stomach
23	chr9:103191600-103206600	Weak transcription	Aorta	Aorta
24	chr9:103191600-103209200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr9:103191600-103209200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr9:103191600-103212800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr9:103191600-103213000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr9:103191600-103214400	Weak transcription	Esophagus	oesophagus
29	chr9:103191800-103202200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:103191800-103204200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr9:103191800-103204200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:103191800-103204200	Weak transcription	Fetal Stomach	stomach
33	chr9:103191800-103206000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:103191800-103206000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:103191800-103206000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:103191800-103217600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr9:103191800-103228000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr9:103192000-103204400	Weak transcription	Fetal Brain Female	brain
39	chr9:103192000-103206200	Weak transcription	Brain Angular Gyrus	brain
40	chr9:103192000-103206400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr9:103192000-103206400	Weak transcription	Brain Anterior Caudate	brain
42	chr9:103192000-103206600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr9:103192000-103208000	Weak transcription	Brain Substantia Nigra	brain
44	chr9:103192000-103214000	Weak transcription	Colon Smooth Muscle	Colon
45	chr9:103192200-103204400	Weak transcription	Left Ventricle	heart
46	chr9:103192200-103210600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr9:103192600-103213200	Weak transcription	Fetal Brain Male	brain
48	chr9:103192800-103202400	Weak transcription	HepG2	liver
49	chr9:103193000-103202200	Weak transcription	Hela-S3	cervix
50	chr9:103193000-103214400	Weak transcription	Pancreas	Pancrea

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