Variant report

Variant	rs540520
Chromosome Location	chr12:120911786-120911787
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr12:120911527-120911938	HEK293-T-REx	kidney:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120903414..120909393-chr12:120910653..120915482,19	MCF-7	breast:
2	chr12:120727751..120732241-chr12:120903536..120914205,12	MCF-7	breast:
3	chr12:120909563..120912110-chr12:120924633..120927390,2	K562	blood:
4	chr12:120910777..120912847-chr12:121016682..121018321,2	MCF-7	breast:
5	chr12:120911060..120912767-chr14:53941405..53944319,2	MCF-7	breast:
6	chr12:120903651..120915747-chr12:120930491..120936868,24	K562	blood:
7	chr12:120908111..120912110-chr12:120923123..120927882,5	K562	blood:
8	chr12:120909586..120912181-chr12:120920227..120921811,2	K562	blood:
9	chr12:120910390..120913098-chr12:120962746..120965463,2	MCF-7	breast:
10	chr12:120911083..120913950-chr12:120960998..120963373,2	K562	blood:
11	chr12:120899786..120915162-chr12:120926090..120939394,54	MCF-7	breast:
12	chr12:120911190..120915382-chr12:120965465..120968340,3	MCF-7	breast:
13	chr12:120905117..120912400-chr12:120930505..120935641,13	K562	blood:
14	chr12:120874424..120877390-chr12:120911060..120913556,3	MCF-7	breast:
15	chr12:120910734..120913987-chr12:120933079..120935604,5	MCF-7	breast:

No data

Variant related genes	Relation type
SRSF9	TF binding region
ENSG00000167272	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000111775	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000241030	Chromatin interaction
ENSG00000088986	Chromatin interaction
ENSG00000111780	Chromatin interaction
ENSG00000111786	Chromatin interaction
ENSG00000110871	Chromatin interaction
ENSG00000248008	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10774556	0.88[ASN][1000 genomes]
rs1167698	0.90[ASN][1000 genomes]
rs1167711	0.87[ASN][1000 genomes]
rs1167712	0.86[ASN][1000 genomes]
rs1167718	0.83[ASN][1000 genomes]
rs1563333	0.95[YRI][hapmap]
rs1616443	0.89[AFR][1000 genomes]
rs2235218	0.95[YRI][hapmap]
rs2292681	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4766966	1.00[YRI][hapmap]
rs4767909	0.86[ASN][1000 genomes]
rs492574	0.82[EUR][1000 genomes]
rs566124	0.94[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs608724	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs636737	0.82[ASN][1000 genomes]
rs7138112	0.88[ASN][1000 genomes]
rs755549	0.88[ASN][1000 genomes]
rs787820	1.00[ASW][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs787947	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs540520	GATC	cis	cerebellum	SCAN
rs540520	HRK	cis	cerebellum	SCAN
rs540520	PXN	cis	parietal	SCAN
rs540520	MORN3	cis	cerebellum	SCAN
rs540520	POP5	cis	lymphoblastoid	seeQTL
rs540520	POP5	cis	cerebellum	SCAN
rs540520	GATC	cis	parietal	SCAN
rs540520	POP5	Cis_1M	lymphoblastoid	RTeQTL
rs540520	GATC	cis	lymphoblastoid	seeQTL
rs540520	COQ5	Cis_1M	lymphoblastoid	RTeQTL
rs540520	COQ5	cis	parietal	SCAN
rs540520	POP5	cis	parietal	SCAN
rs540520	15E1.2	cis	uninvolved skin	skin_eQTL
rs540520	COQ5	cis	Muscle Skeletal	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120908200-120933200	Weak transcription	Aorta	Aorta
2	chr12:120908400-120912000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr12:120908400-120912000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr12:120908400-120912000	Weak transcription	Brain Substantia Nigra	brain
5	chr12:120908400-120912000	Weak transcription	A549	lung
6	chr12:120908400-120912200	Weak transcription	HUVEC	blood vessel
7	chr12:120908400-120912200	Weak transcription	Osteobl	bone
8	chr12:120908400-120912400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr12:120908400-120912400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr12:120908400-120912400	Weak transcription	Fetal Kidney	kidney
11	chr12:120908400-120912400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr12:120908400-120912400	Weak transcription	NHDF-Ad	bronchial
13	chr12:120908400-120912600	Weak transcription	Brain Anterior Caudate	brain
14	chr12:120908400-120917400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:120908400-120919400	Weak transcription	Right Ventricle	heart
16	chr12:120908400-120919800	Weak transcription	Fetal Intestine Large	intestine
17	chr12:120908400-120925800	Weak transcription	Fetal Intestine Small	intestine
18	chr12:120908400-120926000	Weak transcription	HSMMtube	muscle
19	chr12:120908400-120928800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:120908400-120929000	Weak transcription	Psoas Muscle	Psoas
21	chr12:120908400-120932400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr12:120908400-120932400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:120908600-120911800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:120908600-120911800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:120908600-120911800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:120908600-120911800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr12:120908600-120911800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:120908600-120911800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr12:120908600-120912000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:120908600-120912000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:120908600-120912200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:120908600-120912200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:120908600-120912200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:120908600-120912200	Weak transcription	HSMM	muscle
35	chr12:120908600-120912200	Weak transcription	NH-A	brain
36	chr12:120908600-120912400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:120908600-120912400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:120908600-120912400	Weak transcription	NHLF	lung
39	chr12:120908600-120912600	Weak transcription	Ovary	ovary
40	chr12:120908600-120917400	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:120908600-120925400	Weak transcription	Pancreas	Pancrea
42	chr12:120908600-120927200	Weak transcription	Fetal Brain Female	brain
43	chr12:120908600-120928200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:120908600-120928600	Weak transcription	Spleen	Spleen
45	chr12:120908600-120928800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:120908600-120932800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr12:120908600-120932800	Weak transcription	Adipose Nuclei	Adipose
48	chr12:120908600-120932800	Weak transcription	Brain Germinal Matrix	brain
49	chr12:120908600-120932800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:120908600-120933000	Weak transcription	Thymus	Thymus

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