Variant report

Variant	rs10516496
Chromosome Location	chr4:103942165-103942166
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	POLR2A	chr4:103942117-103944541	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:103789727..103791350-chr4:103941608..103944340,2	K562	blood:
2	chr4:103748367..103750223-chr4:103941089..103943490,2	K562	blood:
3	chr4:103421174..103422734-chr4:103941053..103943146,2	K562	blood:

Variant related genes	Relation type
SLC9B1	TF binding region
ENSG00000109320	Chromatin interaction
ENSG00000260651	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000145354	Chromatin interaction
ENSG00000246560	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10006474	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10013062	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10516495	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11929841	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11946020	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13113099	0.80[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.80[TSI][hapmap]
rs13149311	0.86[GIH][hapmap];0.80[JPT][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes]
rs13150953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13151569	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1481279	0.91[GIH][hapmap];0.86[JPT][hapmap]
rs223317	0.91[CEU][hapmap]
rs223331	0.91[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs223361	0.91[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap]
rs223366	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs223374	0.91[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs2866416	0.96[CEU][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34475639	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698875	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698876	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699048	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6533039	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6816370	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6843738	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7665026	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7674212	0.89[GIH][hapmap]
rs7691873	0.91[GIH][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv461598	chr4:103807720-103953389	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv594978	chr4:103807720-103953389	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv830021	chr4:103934454-104100588	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10516496	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs10516496	MANBA	cis	multi-tissue	Pritchard
rs10516496	KRT8P46	cis	lung	GTEx
rs10516496	MANBA	cis	cerebellum	SCAN
rs10516496	LRRC37A15P	cis	Thyroid	GTEx
rs10516496	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs10516496	CISD2	cis	cerebellum	SCAN
rs10516496	MANBA	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103940000-103950600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:103941000-103953800	Weak transcription	Gastric	stomach
3	chr4:103941200-103944200	Weak transcription	Spleen	Spleen
4	chr4:103941400-103942400	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr4:103941400-103945200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:103941400-103946200	Weak transcription	Left Ventricle	heart
7	chr4:103941400-103946600	Weak transcription	NHDF-Ad	bronchial
8	chr4:103941400-103948400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr4:103941400-103949800	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:103941400-103950400	Weak transcription	Fetal Brain Female	brain
11	chr4:103941400-103951200	Weak transcription	Fetal Heart	heart
12	chr4:103941400-103951400	Weak transcription	HepG2	liver
13	chr4:103941400-103953800	Weak transcription	Brain Germinal Matrix	brain
14	chr4:103941400-103957200	Weak transcription	Fetal Brain Male	brain
15	chr4:103941400-103964400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:103941400-103964800	Weak transcription	HSMM	muscle
17	chr4:103941400-103965200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:103941400-103967200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:103941400-103967800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:103941400-103968000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:103941400-103968000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:103941400-103969000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:103941400-103969200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr4:103941400-103974000	Weak transcription	Esophagus	oesophagus
25	chr4:103941400-103975200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:103941400-103989400	Weak transcription	NH-A	brain
27	chr4:103941400-103996600	Weak transcription	Lung	lung
28	chr4:103941600-103942400	Enhancers	Psoas Muscle	Psoas
29	chr4:103941600-103944000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:103941600-103945400	Weak transcription	Liver	Liver
31	chr4:103941600-103946000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:103941600-103946800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:103941600-103947200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:103941600-103950200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:103941600-103951400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:103941600-103952600	Weak transcription	Hela-S3	cervix
37	chr4:103941600-103957000	Weak transcription	Ovary	ovary
38	chr4:103941600-103957000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr4:103941600-103963000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:103941600-103965400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr4:103941600-103965400	Weak transcription	NHEK	skin
42	chr4:103941600-103968000	Weak transcription	Fetal Muscle Leg	muscle
43	chr4:103941600-103969200	Weak transcription	Adipose Nuclei	Adipose
44	chr4:103941600-103969200	Weak transcription	Fetal Thymus	thymus
45	chr4:103941600-103989000	Weak transcription	HMEC	breast
46	chr4:103941800-103946000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr4:103941800-103946200	Weak transcription	Primary B cells from cord blood	blood
48	chr4:103941800-103946800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:103941800-103947200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr4:103941800-103947200	Weak transcription	Brain Angular Gyrus	brain

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