Variant report

Variant	rs1557769
Chromosome Location	chr12:120800696-120800697
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	RFX5	chr12:120798645-120800948	SK-N-SH	brain:	n/a	chr12:120799690-120799704 chr12:120799697-120799706 chr12:120799692-120799707 chr12:120799689-120799704 chr12:120799691-120799708 chr12:120799695-120799709 chr12:120799692-120799707 chr12:120799357-120799372 chr12:120799693-120799702 chr12:120799692-120799707 chr12:120799357-120799372 chr12:120800331-120800339 chr12:120799357-120799372
2	ZNF263	chr12:120800423-120800723	HEK293-T-REx	kidney:	n/a	chr12:120800567-120800588
3	REST	chr12:120798813-120800796	H1-neurons	neurons:	n/a	chr12:120799888-120799908 chr12:120799932-120799945 chr12:120800492-120800505 chr12:120799711-120799724 chr12:120798991-120798999 chr12:120799810-120799823

No.	Distal block	Cell Line	Cell type
1	chr12:120799434..120804968-chr12:120812300..120816168,6	K562	blood:
2	chr12:120800502..120802375-chr12:120882088..120884770,2	MCF-7	breast:
3	chr12:120728315..120730053-chr12:120799765..120801702,2	MCF-7	breast:
4	chr12:120799433..120803407-chr12:120804628..120808209,5	K562	blood:

Variant related genes	Relation type
MSI1	TF binding region
ENSG00000135097	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000170855	Chromatin interaction
ENSG00000257218	Chromatin interaction
ENSG00000239881	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10849743	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11065075	0.85[EUR][1000 genomes]
rs11065091	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11065094	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11614028	0.87[EUR][1000 genomes]
rs1179387	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs206951	0.91[EUR][1000 genomes]
rs206966	0.83[EUR][1000 genomes]
rs2522129	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2522138	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2522141	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2696027	0.81[ASN][1000 genomes]
rs3742038	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5637	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67706074	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7314115	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73416934	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
2	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120780800-120803200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:120789400-120802000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr12:120795800-120804200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:120796200-120805000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:120798400-120801600	Enhancers	Fetal Brain Male	brain
6	chr12:120799000-120800800	Enhancers	Stomach Mucosa	stomach
7	chr12:120799000-120801200	Enhancers	Pancreas	Pancrea
8	chr12:120799600-120804000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
9	chr12:120799600-120804200	Weak transcription	Left Ventricle	heart
10	chr12:120799800-120800800	Flanking Active TSS	Fetal Brain Female	brain
11	chr12:120800000-120800800	Enhancers	Brain Angular Gyrus	brain
12	chr12:120800000-120800800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr12:120800000-120801200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:120800000-120801200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:120800000-120801400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:120800000-120801800	Enhancers	Fetal Muscle Leg	muscle
17	chr12:120800000-120802200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:120800000-120805000	Enhancers	Fetal Intestine Large	intestine
19	chr12:120800200-120800800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
20	chr12:120800200-120800800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
21	chr12:120800200-120800800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
22	chr12:120800200-120800800	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr12:120800200-120800800	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr12:120800200-120800800	Enhancers	Brain Substantia Nigra	brain
25	chr12:120800200-120801000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:120800200-120801000	Genic enhancers	Fetal Lung	lung
27	chr12:120800200-120801000	Genic enhancers	Fetal Stomach	stomach
28	chr12:120800200-120801200	Enhancers	Gastric	stomach
29	chr12:120800200-120801400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr12:120800200-120801600	Enhancers	Brain Cingulate Gyrus	brain
31	chr12:120800200-120802200	Genic enhancers	H1 Cell Line	embryonic stem cell
32	chr12:120800200-120802600	Enhancers	Brain Anterior Caudate	brain
33	chr12:120800200-120803400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:120800200-120804000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:120800200-120804000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr12:120800200-120805200	Genic enhancers	Fetal Intestine Small	intestine
37	chr12:120800200-120805400	Weak transcription	Ovary	ovary
38	chr12:120800400-120800800	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr12:120800400-120801200	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:120800400-120801400	Enhancers	Brain Hippocampus Middle	brain
41	chr12:120800400-120801800	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr12:120800400-120802200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
43	chr12:120800400-120802200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:120800400-120803000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:120800400-120803000	Weak transcription	Fetal Kidney	kidney
46	chr12:120800400-120804800	Enhancers	Duodenum Mucosa	Duodenum
47	chr12:120800400-120805000	Weak transcription	Esophagus	oesophagus
48	chr12:120800400-120805600	Weak transcription	Right Atrium	heart
49	chr12:120800600-120801000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:120800600-120801400	Weak transcription	H9 Cell Line	embryonic stem cell

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