Variant report

Variant	rs1465207
Chromosome Location	chr12:120800229-120800230
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	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	MXI1	chr12:120798826-120800303	SK-N-SH	brain:	n/a	chr12:120799691-120799706 chr12:120799693-120799708
3	POLR2A	chr12:120799144-120800413	H1-neurons	neurons:	n/a	n/a
4	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
5	POLR2A	chr12:120798842-120800479	H1-hESC	embryonic stem cell:	n/a	n/a

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

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

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10735072	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10774544	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10849744	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065080	0.89[EUR][1000 genomes]
rs11065084	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11065085	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11065086	0.92[EUR][1000 genomes]
rs11065097	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1179435	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2238160	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2239198	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2522137	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34570155	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35842297	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs67278663	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68012838	0.85[EUR][1000 genomes]
rs7959801	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9669536	0.90[EUR][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:63 , 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	chr12:120784800-120800400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:120789400-120802000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:120795800-120804200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:120796200-120805000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:120798400-120801600	Enhancers	Fetal Brain Male	brain
7	chr12:120799000-120800600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr12:120799000-120800600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:120799000-120800600	Enhancers	Fetal Heart	heart
10	chr12:120799000-120800800	Enhancers	Stomach Mucosa	stomach
11	chr12:120799000-120801200	Enhancers	Pancreas	Pancrea
12	chr12:120799400-120800400	Enhancers	Esophagus	oesophagus
13	chr12:120799600-120800400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:120799600-120800400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
15	chr12:120799600-120800400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
16	chr12:120799600-120804000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
17	chr12:120799600-120804200	Weak transcription	Left Ventricle	heart
18	chr12:120799800-120800400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:120799800-120800400	Flanking Active TSS	Brain Hippocampus Middle	brain
20	chr12:120799800-120800400	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr12:120799800-120800400	Enhancers	Placenta	Placenta
22	chr12:120799800-120800600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:120799800-120800600	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr12:120799800-120800800	Flanking Active TSS	Fetal Brain Female	brain
25	chr12:120800000-120800400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:120800000-120800400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:120800000-120800400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
28	chr12:120800000-120800400	Flanking Active TSS	Fetal Kidney	kidney
29	chr12:120800000-120800600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:120800000-120800800	Enhancers	Brain Angular Gyrus	brain
31	chr12:120800000-120800800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr12:120800000-120801200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:120800000-120801200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:120800000-120801400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:120800000-120801800	Enhancers	Fetal Muscle Leg	muscle
36	chr12:120800000-120802200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:120800000-120805000	Enhancers	Fetal Intestine Large	intestine
38	chr12:120800200-120800400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
39	chr12:120800200-120800400	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr12:120800200-120800400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
41	chr12:120800200-120800400	Bivalent Enhancer	Colonic Mucosa	Colon
42	chr12:120800200-120800400	Enhancers	Right Atrium	heart
43	chr12:120800200-120800600	Genic enhancers	H9 Cell Line	embryonic stem cell
44	chr12:120800200-120800600	Genic enhancers	Right Ventricle	heart
45	chr12:120800200-120800800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
46	chr12:120800200-120800800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
47	chr12:120800200-120800800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
48	chr12:120800200-120800800	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr12:120800200-120800800	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr12:120800200-120800800	Enhancers	Brain Substantia Nigra	brain

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