Variant report

Variant	rs12057476
Chromosome Location	chr1:93582744-93582745
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93582432..93585067-chr1:93594347..93596208,2	K562	blood:

Variant related genes	Relation type
ENSG00000143033	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10874765	1.00[YRI][hapmap]
rs10874767	0.96[TSI][hapmap]
rs11164874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11164878	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11164882	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11586323	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12064785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12066315	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12067005	0.91[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12070900	0.94[YRI][hapmap]
rs12085959	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs12087466	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12088338	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12094547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1414367	1.00[ASW][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1535698	1.00[YRI][hapmap]
rs17131699	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2391227	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2484485	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2749735	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2783492	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2783498	0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2783506	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2815408	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2815409	1.00[ASW][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2815410	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2815411	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2815412	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2815413	0.82[EUR][1000 genomes]
rs2815414	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36057148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs504810	0.91[CEU][hapmap]
rs505531	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs506556	0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs519723	0.96[TSI][hapmap]
rs522999	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs546	1.00[ASW][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55701931	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs571212	0.92[TSI][hapmap]
rs573056	0.96[TSI][hapmap]
rs581825	0.81[EUR][1000 genomes]
rs615416	0.82[EUR][1000 genomes]
rs626714	0.96[TSI][hapmap]
rs629153	1.00[YRI][hapmap]
rs633789	0.96[TSI][hapmap]
rs658178	1.00[YRI][hapmap]
rs658877	0.82[EUR][1000 genomes]
rs6667701	0.96[TSI][hapmap]
rs667680	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs668944	0.96[TSI][hapmap]
rs671559	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71510760	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs797660	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs12057476	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs12057476	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs12057476	TMED5	cis	multi-tissue	Pritchard
rs12057476	LOC646848	cis	normal skin	skin_eQTL
rs12057476	RP4-717I23.3	cis	Artery Aorta	GTEx
rs12057476	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12057476	RP4-717I23.3	cis	Artery Tibial	GTEx
rs12057476	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs12057476	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs12057476	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs12057476	RP4-717I23.3	cis	Whole Blood	GTEx
rs12057476	RP4-717I23.3	cis	Thyroid	GTEx
rs12057476	DR1	cis	multi-tissue	Pritchard
rs12057476	LOC646848	cis	multi-tissue	Pritchard
rs12057476	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs12057476	RP4-717I23.3	cis	Stomach	GTEx
rs12057476	RP4-717I23.3	cis	lung	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93546200-93602200	Weak transcription	Aorta	Aorta
2	chr1:93547600-93600000	Weak transcription	HSMMtube	muscle
3	chr1:93548000-93601800	Weak transcription	NHLF	lung
4	chr1:93549000-93582800	Weak transcription	NHEK	skin
5	chr1:93565200-93625200	Weak transcription	Stomach Mucosa	stomach
6	chr1:93568400-93584200	Weak transcription	Fetal Brain Male	brain
7	chr1:93571400-93602200	Weak transcription	Colonic Mucosa	Colon
8	chr1:93572400-93599600	Weak transcription	Spleen	Spleen
9	chr1:93573400-93627000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:93573600-93586000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:93573800-93609000	Strong transcription	Fetal Thymus	thymus
12	chr1:93574200-93609000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:93574600-93584800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:93574600-93585800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:93574600-93609000	Strong transcription	Dnd41	blood
16	chr1:93574600-93630200	Weak transcription	Right Ventricle	heart
17	chr1:93575200-93589800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:93575800-93589200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:93577200-93592800	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:93577200-93597000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:93577600-93585200	Strong transcription	Primary hematopoietic stem cells	blood
22	chr1:93577600-93586600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:93577600-93586800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:93577600-93588800	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:93577600-93591400	Weak transcription	Fetal Heart	heart
26	chr1:93577800-93601600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:93578200-93587200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:93578200-93588200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:93578400-93583600	Strong transcription	GM12878-XiMat	blood
30	chr1:93578400-93583800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:93578400-93587400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr1:93578400-93587600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:93578600-93586600	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr1:93578600-93586800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:93578600-93586800	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:93578800-93613600	Weak transcription	Psoas Muscle	Psoas
37	chr1:93578800-93620600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:93579600-93586800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:93579600-93587200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr1:93579600-93595400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:93579800-93583800	Strong transcription	K562	blood
42	chr1:93579800-93586600	Strong transcription	Liver	Liver
43	chr1:93579800-93587200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr1:93579800-93588000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:93580000-93582800	Strong transcription	NH-A	brain
46	chr1:93580000-93583000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:93580000-93585800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr1:93580000-93586400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:93580000-93587600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:93580000-93587600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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