Variant report

Variant	rs9468300
Chromosome Location	chr6:28126840-28126841
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	MAFF	chr6:28126793-28127160	HepG2	liver:	n/a	chr6:28126998-28127016
2	MAFK	chr6:28126739-28127168	HepG2	liver:	n/a	chr6:28126999-28127014
3	POLR2A	chr6:28126735-28127109	K562	blood:	n/a	n/a
4	MAFK	chr6:28126819-28127124	HepG2	liver:	n/a	chr6:28126999-28127014

No.	Distal block	Cell Line	Cell type
1	chr6:28125801..28127363-chr6:28321236..28323956,2	K562	blood:
2	chr6:28123814..28127581-chr6:28129241..28131272,3	MCF-7	breast:
3	chr6:28124753..28127953-chr6:28128096..28131158,4	K562	blood:
4	chr6:28126788..28129229-chr6:28184991..28186834,2	MCF-7	breast:

Variant related genes	Relation type
ZNF192P1	TF binding region
ENSG00000235109	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000226314	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1321505	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13437126	0.91[ASN][1000 genomes]
rs13437444	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16893735	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs34130214	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34712084	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3734571	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3757188	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4713138	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4713139	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4713140	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs735765	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8180562	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9348792	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9357064	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9366717	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9368560	0.85[ASN][1000 genomes]
rs9368561	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380064	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9380069	0.80[EUR][1000 genomes]
rs9393889	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9393902	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9393908	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9461432	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9461439	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9468287	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9468301	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9468300	RP5-874C20.3	cis	Thyroid	GTEx
rs9468300	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs9468300	AL022393.7	cis	Muscle Skeletal	GTEx
rs9468300	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9468300	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28111400-28129200	Weak transcription	Right Atrium	heart
2	chr6:28111800-28127000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:28113200-28127200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:28115200-28127200	Strong transcription	Fetal Brain Female	brain
5	chr6:28115400-28127000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:28115400-28127000	Strong transcription	Fetal Muscle Trunk	muscle
7	chr6:28115800-28127400	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr6:28116000-28127000	Strong transcription	Brain Hippocampus Middle	brain
9	chr6:28116000-28127200	Strong transcription	Stomach Smooth Muscle	stomach
10	chr6:28116200-28127000	Strong transcription	Fetal Lung	lung
11	chr6:28121400-28127000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:28121400-28127200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:28121600-28129000	Weak transcription	Fetal Intestine Small	intestine
14	chr6:28121600-28129200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:28121800-28127000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:28121800-28127000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:28121800-28127400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:28121800-28127400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:28121800-28129200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:28122000-28129200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:28122000-28129200	Weak transcription	Stomach Mucosa	stomach
22	chr6:28122200-28127600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:28122200-28129000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:28122200-28129000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr6:28122200-28129200	Weak transcription	Small Intestine	intestine
26	chr6:28122600-28129000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr6:28122600-28129200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:28122600-28129200	Weak transcription	Esophagus	oesophagus
29	chr6:28122600-28129200	Weak transcription	Fetal Stomach	stomach
30	chr6:28122800-28129200	Weak transcription	Colonic Mucosa	Colon
31	chr6:28122800-28129200	Weak transcription	Gastric	stomach
32	chr6:28122800-28129200	Weak transcription	HSMMtube	muscle
33	chr6:28122800-28129400	Weak transcription	Spleen	Spleen
34	chr6:28123000-28128000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:28123000-28129000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr6:28123000-28129200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:28123000-28129200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:28123000-28129200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:28123000-28129200	Weak transcription	Lung	lung
40	chr6:28123000-28129200	Weak transcription	Pancreas	Pancrea
41	chr6:28123000-28129200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:28123000-28129200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr6:28123000-28129200	Weak transcription	Hela-S3	cervix
44	chr6:28123200-28129200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr6:28123200-28129200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr6:28123200-28129200	Weak transcription	Fetal Thymus	thymus
47	chr6:28123400-28129000	Weak transcription	HMEC	breast
48	chr6:28123400-28129200	Weak transcription	Brain Angular Gyrus	brain
49	chr6:28123400-28129200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr6:28123600-28129000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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