Variant report

Variant	rs10009947
Chromosome Location	chr4:76864459-76864460
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	chr4:76863857..76865771-chr4:76874139..76877133,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10021434	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10031733	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10518143	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12374321	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12374370	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13105416	0.82[EUR][1000 genomes]
rs13112512	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13118503	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13129896	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17001247	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1857821	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2242470	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271528	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276886	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28375800	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28422144	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28451731	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28532601	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28535831	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28588114	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28595360	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28647886	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2869462	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34630680	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34740469	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3733238	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3796484	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4241577	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4859567	0.82[EUR][1000 genomes]
rs4859568	0.82[EUR][1000 genomes]
rs4859569	0.82[EUR][1000 genomes]
rs4859570	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859571	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859572	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859573	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859577	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859578	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859580	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55876513	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66498356	0.95[ASN][1000 genomes]
rs6847815	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs884004	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv3396277	chr4:76861228-76865426	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10009947	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs10009947	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs10009947	NAAA	cis	Esophagus Mucosa	GTEx
rs10009947	NAAA	cis	Artery Aorta	GTEx
rs10009947	NAAA	cis	Adipose Subcutaneous	GTEx
rs10009947	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs10009947	NAAA	cis	Esophagus Muscularis	GTEx
rs10009947	NAAA	cis	Muscle Skeletal	GTEx
rs10009947	NAAA	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76862000-76868200	Weak transcription	Fetal Lung	lung
2	chr4:76862000-76871600	Weak transcription	Fetal Kidney	kidney
3	chr4:76862000-76875600	Weak transcription	Fetal Heart	heart
4	chr4:76862000-76896600	Weak transcription	Stomach Mucosa	stomach
5	chr4:76862200-76864600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:76862200-76867400	Weak transcription	NHDF-Ad	bronchial
7	chr4:76862200-76868000	Weak transcription	GM12878-XiMat	blood
8	chr4:76862200-76868200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:76862200-76871000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:76862200-76871000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:76862200-76875200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:76862200-76876400	Weak transcription	Gastric	stomach
13	chr4:76862200-76876600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:76862200-76886600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:76862400-76864600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:76862400-76864600	Weak transcription	HMEC	breast
17	chr4:76862400-76864800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:76862400-76864800	Weak transcription	HSMM	muscle
19	chr4:76862400-76867600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:76862400-76867800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:76862400-76868000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:76862400-76868000	Weak transcription	Lung	lung
23	chr4:76862400-76868000	Weak transcription	HUVEC	blood vessel
24	chr4:76862400-76868400	Weak transcription	Ovary	ovary
25	chr4:76862400-76868400	Weak transcription	HSMMtube	muscle
26	chr4:76862400-76868600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:76862400-76873400	Weak transcription	Colon Smooth Muscle	Colon
28	chr4:76862400-76875400	Weak transcription	Spleen	Spleen
29	chr4:76862400-76876600	Weak transcription	Aorta	Aorta
30	chr4:76862400-76876600	Weak transcription	Small Intestine	intestine
31	chr4:76862600-76864800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:76862600-76864800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:76862600-76864800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr4:76862600-76864800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:76862600-76864800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:76862600-76865200	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr4:76862600-76865200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:76862600-76866200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:76862600-76867400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr4:76862600-76867400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:76862600-76867400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:76862600-76867400	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:76862600-76867400	Weak transcription	Fetal Intestine Large	intestine
44	chr4:76862600-76867400	Weak transcription	Osteobl	bone
45	chr4:76862600-76867600	Weak transcription	Thymus	Thymus
46	chr4:76862600-76867800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:76862600-76867800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:76862600-76867800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr4:76862600-76867800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:76862600-76867800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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