Variant report

Variant	rs2039590
Chromosome Location	chr1:150813315-150813316
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	GATA1	chr1:150813193-150813663	PBDE	blood:	n/a	chr1:150813405-150813414 chr1:150813404-150813414 chr1:150813405-150813412 chr1:150813402-150813412
2	SPI1	chr1:150813086-150813430	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:150807087..150808986-chr1:150811625..150814317,2	MCF-7	breast:
2	chr1:150800531..150803502-chr1:150811550..150815655,4	MCF-7	breast:

Variant related genes	Relation type
ARNT	TF binding region
ENSG00000143437	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1081512	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11204725	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11204735	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204737	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1136774	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12125650	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12126004	0.88[EUR][1000 genomes]
rs12402006	0.91[EUR][1000 genomes]
rs12404199	0.91[EUR][1000 genomes]
rs12410050	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12568757	0.87[EUR][1000 genomes]
rs12725806	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12758227	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2089081	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34002273	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3894771	0.81[EUR][1000 genomes]
rs486836	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4970932	0.85[EUR][1000 genomes]
rs4970976	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7412746	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7534124	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv437169	chr1:150738197-150816886	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription 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	156 gene(s)	inside rSNPs	diseases
5	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	nsv872420	chr1:150786038-150847647	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1010875	chr1:150796816-150845827	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	esv1793983	chr1:150804748-150825924	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs2039590	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs2039590	CTSS	cis	multi-tissue	Pritchard
rs2039590	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs2039590	RP11-316M1.12	cis	lung	GTEx
rs2039590	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs2039590	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs2039590	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs2039590	RP11-316M1.12	cis	Thyroid	GTEx
rs2039590	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs2039590	HORMAD1	cis	Esophagus Mucosa	GTEx
rs2039590	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs2039590	RP11-316M1.12	cis	Whole Blood	GTEx
rs2039590	CTSK	cis	multi-tissue	Pritchard
rs2039590	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs2039590	CTSS	cis	Thyroid	GTEx
rs2039590	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs2039590	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs2039590	RP11-316M1.12	cis	Artery Tibial	GTEx
rs2039590	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs2039590	HORMAD1	cis	Nerve Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150783200-150816600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:150783200-150816800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:150792200-150814800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:150792600-150815400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:150793000-150816400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:150793200-150823200	Strong transcription	Placenta	Placenta
7	chr1:150793600-150815800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:150793800-150813800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:150794000-150813600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:150797000-150814400	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:150797400-150813400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:150797600-150813400	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr1:150797600-150815600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:150798200-150815600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:150799600-150816600	Strong transcription	HSMM	muscle
16	chr1:150799800-150817800	Strong transcription	Primary B cells from cord blood	blood
17	chr1:150801800-150814800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:150801800-150818600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:150801800-150824600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:150802800-150815200	Strong transcription	Fetal Lung	lung
21	chr1:150805800-150824600	Weak transcription	HMEC	breast
22	chr1:150807200-150814200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:150807200-150820800	Weak transcription	Spleen	Spleen
24	chr1:150807400-150824600	Weak transcription	A549	lung
25	chr1:150807400-150847000	Weak transcription	Colonic Mucosa	Colon
26	chr1:150808000-150821600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:150808800-150847000	Weak transcription	Psoas Muscle	Psoas
28	chr1:150809000-150816400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:150809000-150819200	Weak transcription	K562	blood
30	chr1:150809000-150823000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:150809000-150824400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:150809000-150824600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:150809200-150814200	Weak transcription	Stomach Mucosa	stomach
34	chr1:150809200-150820600	Weak transcription	Brain Germinal Matrix	brain
35	chr1:150809200-150824600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:150809200-150846800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:150809400-150813800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:150809400-150815000	Strong transcription	Liver	Liver
39	chr1:150809400-150821000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:150809400-150821000	Weak transcription	Thymus	Thymus
41	chr1:150809400-150823200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:150809600-150820400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:150809600-150846000	Weak transcription	Pancreas	Pancrea
44	chr1:150809800-150814000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:150810000-150824800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr1:150810200-150824600	Weak transcription	NHLF	lung
47	chr1:150810400-150846600	Weak transcription	Fetal Heart	heart
48	chr1:150810600-150815000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:150811000-150814600	Strong transcription	Hela-S3	cervix
50	chr1:150811400-150815400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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