Variant report

Variant	rs7296418
Chromosome Location	chr12:123457619-123457620
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123379576..123381304-chr12:123456345..123457944,2	K562	blood:
2	chr12:57912351..57915137-chr12:123457151..123459849,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000208028	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000139722	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1051434	0.91[CEU][hapmap];0.95[TSI][hapmap]
rs10773921	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10848428	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap]
rs11060853	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11608811	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11613937	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12425009	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12425850	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1615350	0.81[TSI][hapmap]
rs1617156	0.81[MEX][hapmap];0.87[YRI][hapmap]
rs1727293	0.87[CEU][hapmap];0.86[CHB][hapmap];0.95[TSI][hapmap]
rs1727295	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs1727302	0.81[TSI][hapmap]
rs1727307	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap]
rs1790094	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap]
rs1790106	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap]
rs1790121	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap]
rs1984658	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28755851	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3741530	0.91[CEU][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759115	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3897102	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4148863	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap]
rs4148866	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4275659	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs520088	0.86[YRI][hapmap]
rs55742290	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs585522	0.85[MEX][hapmap];0.87[YRI][hapmap]
rs61955196	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61955214	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs641760	0.81[MEX][hapmap]
rs655293	0.81[MEX][hapmap];0.83[YRI][hapmap]
rs7135296	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7299943	0.81[MEX][hapmap]
rs7305511	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7957096	0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs883263	0.81[MEX][hapmap];0.83[YRI][hapmap]
rs883562	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs883563	0.83[AMR][1000 genomes]
rs884956	0.90[CHB][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs937564	0.81[MEX][hapmap];0.83[YRI][hapmap]
rs949143	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv899577	chr12:123435248-123484474	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Platelet counts	21507922	GWAS catalog

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7296418	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs7296418	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs7296418	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs7296418	SBNO1	cis	lymphoblastoid	seeQTL
rs7296418	ABCB9	cis	Heart Left Ventricle	GTEx
rs7296418	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs7296418	EPS8	trans	lymphoblastoid	seeQTL
rs7296418	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs7296418	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123451000-123458600	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:123451400-123458200	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr12:123451400-123458400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:123451400-123458400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:123451400-123458400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:123451400-123458400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:123451400-123458400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:123451400-123458400	Weak transcription	Brain Anterior Caudate	brain
9	chr12:123451400-123458400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:123451400-123458400	Weak transcription	Brain Germinal Matrix	brain
11	chr12:123451400-123458400	Weak transcription	Fetal Muscle Leg	muscle
12	chr12:123451400-123458600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:123451400-123458600	Weak transcription	Right Atrium	heart
14	chr12:123451400-123458600	Weak transcription	Thymus	Thymus
15	chr12:123451600-123458200	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr12:123451600-123458400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr12:123451600-123458400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:123451600-123458400	Weak transcription	Adipose Nuclei	Adipose
19	chr12:123451600-123458400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:123451600-123458400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr12:123451600-123458600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr12:123451600-123458600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:123451600-123458600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:123451600-123458600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:123451600-123458800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr12:123451800-123458400	Weak transcription	A549	lung
27	chr12:123451800-123458400	Weak transcription	K562	blood
28	chr12:123451800-123458600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:123451800-123458600	Weak transcription	Stomach Mucosa	stomach
30	chr12:123452000-123458400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:123452000-123458400	Weak transcription	Brain Angular Gyrus	brain
32	chr12:123452400-123458400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr12:123453200-123458200	Weak transcription	HepG2	liver
34	chr12:123453800-123458400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:123453800-123458600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:123453800-123458600	Weak transcription	NHEK	skin
37	chr12:123454400-123458200	Weak transcription	Placenta	Placenta
38	chr12:123454400-123458400	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:123454600-123458400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:123454600-123458400	Weak transcription	Brain Substantia Nigra	brain
41	chr12:123454600-123458600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr12:123454600-123458600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:123454600-123458600	Weak transcription	Fetal Lung	lung
44	chr12:123454600-123458600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr12:123454600-123458800	Weak transcription	Fetal Heart	heart
46	chr12:123454800-123458400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:123454800-123458400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:123454800-123458400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr12:123454800-123458400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:123455200-123458400	Weak transcription	Fetal Muscle Trunk	muscle

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