Variant report

Variant	rs11946020
Chromosome Location	chr4:103944742-103944743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103943642..103947112-chr4:103947295..103951085,6	K562	blood:
2	chr4:103943064..103945242-chr4:103946803..103948795,3	K562	blood:
3	chr4:103422064..103424246-chr4:103943211..103944859,2	K562	blood:
4	chr4:103422746..103425460-chr4:103943211..103945409,2	K562	blood:
5	chr4:103939107..103942510-chr4:103943069..103945655,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109320	Chromatin interaction
ENSG00000164037	Chromatin interaction
ENSG00000260651	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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10013062	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10516495	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10516496	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]
rs11929841	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13113099	0.91[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs13149311	0.86[GIH][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs13150953	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13151569	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1481279	0.91[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs223317	0.95[CEU][hapmap]
rs223331	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs223361	0.95[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap]
rs223366	0.89[CHB][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.89[YRI][hapmap]
rs223374	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs2866416	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34475639	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4698875	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4698876	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4699048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6533039	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6816370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6843738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7665026	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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
rs11946020	MANBA	cis	multi-tissue	Pritchard
rs11946020	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs11946020	MANBA	cis	cerebellum	SCAN
rs11946020	MANBA	cis	parietal	SCAN
rs11946020	KRT8P46	cis	lung	GTEx
rs11946020	CISD2	cis	cerebellum	SCAN
rs11946020	LRRC37A15P	cis	Thyroid	GTEx
rs11946020	MANBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 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	chr4:103941400-103945200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:103941400-103946200	Weak transcription	Left Ventricle	heart
5	chr4:103941400-103946600	Weak transcription	NHDF-Ad	bronchial
6	chr4:103941400-103948400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:103941400-103949800	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:103941400-103950400	Weak transcription	Fetal Brain Female	brain
9	chr4:103941400-103951200	Weak transcription	Fetal Heart	heart
10	chr4:103941400-103951400	Weak transcription	HepG2	liver
11	chr4:103941400-103953800	Weak transcription	Brain Germinal Matrix	brain
12	chr4:103941400-103957200	Weak transcription	Fetal Brain Male	brain
13	chr4:103941400-103964400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:103941400-103964800	Weak transcription	HSMM	muscle
15	chr4:103941400-103965200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:103941400-103967200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:103941400-103967800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:103941400-103968000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:103941400-103968000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:103941400-103969000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:103941400-103969200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr4:103941400-103974000	Weak transcription	Esophagus	oesophagus
23	chr4:103941400-103975200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:103941400-103989400	Weak transcription	NH-A	brain
25	chr4:103941400-103996600	Weak transcription	Lung	lung
26	chr4:103941600-103945400	Weak transcription	Liver	Liver
27	chr4:103941600-103946000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr4:103941600-103946800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:103941600-103947200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:103941600-103950200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:103941600-103951400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr4:103941600-103952600	Weak transcription	Hela-S3	cervix
33	chr4:103941600-103957000	Weak transcription	Ovary	ovary
34	chr4:103941600-103957000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr4:103941600-103963000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:103941600-103965400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:103941600-103965400	Weak transcription	NHEK	skin
38	chr4:103941600-103968000	Weak transcription	Fetal Muscle Leg	muscle
39	chr4:103941600-103969200	Weak transcription	Adipose Nuclei	Adipose
40	chr4:103941600-103969200	Weak transcription	Fetal Thymus	thymus
41	chr4:103941600-103989000	Weak transcription	HMEC	breast
42	chr4:103941800-103946000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:103941800-103946200	Weak transcription	Primary B cells from cord blood	blood
44	chr4:103941800-103946800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr4:103941800-103947200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr4:103941800-103947200	Weak transcription	Brain Angular Gyrus	brain
47	chr4:103941800-103951600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr4:103941800-103953800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr4:103941800-103955000	Weak transcription	Brain Anterior Caudate	brain
50	chr4:103941800-103964200	Weak transcription	GM12878-XiMat	blood

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