Variant report

Variant	rs34475639
Chromosome Location	chr4:103954851-103954852
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10006474	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10013062	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10516495	0.82[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10516496	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]
rs11929841	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11946020	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]
rs13113099	0.91[GIH][hapmap];0.85[JPT][hapmap];0.80[TSI][hapmap]
rs13149311	0.86[GIH][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs13150953	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13151569	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1481279	0.91[GIH][hapmap];0.86[JPT][hapmap]
rs223317	0.95[CEU][hapmap]
rs223331	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs223361	0.95[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap]
rs223366	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs223374	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs2866416	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4698875	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698876	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699048	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6533039	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6816370	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6843738	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7665026	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7674212	0.88[GIH][hapmap]
rs7691873	0.91[GIH][hapmap];0.86[JPT][hapmap]

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	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	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
4	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
rs34475639	LRRC37A15P	cis	Thyroid	GTEx
rs34475639	KRT8P46	cis	lung	GTEx
rs34475639	MANBA	cis	cerebellum	SCAN
rs34475639	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs34475639	CISD2	cis	cerebellum	SCAN
rs34475639	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs34475639	MANBA	cis	multi-tissue	Pritchard
rs34475639	MANBA	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103941400-103957200	Weak transcription	Fetal Brain Male	brain
2	chr4:103941400-103964400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:103941400-103964800	Weak transcription	HSMM	muscle
4	chr4:103941400-103965200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:103941400-103967200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:103941400-103967800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:103941400-103968000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:103941400-103968000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr4:103941400-103969000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:103941400-103969200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:103941400-103974000	Weak transcription	Esophagus	oesophagus
12	chr4:103941400-103975200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:103941400-103989400	Weak transcription	NH-A	brain
14	chr4:103941400-103996600	Weak transcription	Lung	lung
15	chr4:103941600-103957000	Weak transcription	Ovary	ovary
16	chr4:103941600-103957000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr4:103941600-103963000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:103941600-103965400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:103941600-103965400	Weak transcription	NHEK	skin
20	chr4:103941600-103968000	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:103941600-103969200	Weak transcription	Adipose Nuclei	Adipose
22	chr4:103941600-103969200	Weak transcription	Fetal Thymus	thymus
23	chr4:103941600-103989000	Weak transcription	HMEC	breast
24	chr4:103941800-103955000	Weak transcription	Brain Anterior Caudate	brain
25	chr4:103941800-103964200	Weak transcription	GM12878-XiMat	blood
26	chr4:103941800-103964400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr4:103941800-103965200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:103941800-103965400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr4:103941800-103969600	Weak transcription	Brain Hippocampus Middle	brain
30	chr4:103941800-103994600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:103942000-103964400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:103942000-103964800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr4:103942000-103965200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr4:103942000-103969600	Weak transcription	Primary T cells from cord blood	blood
35	chr4:103942000-103994400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:103942000-103995200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr4:103942400-103964400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr4:103946200-103956400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:103947600-103968000	Weak transcription	NHDF-Ad	bronchial
40	chr4:103947800-103965000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr4:103947800-103996000	Weak transcription	Brain Angular Gyrus	brain
42	chr4:103948200-103969600	Weak transcription	Left Ventricle	heart
43	chr4:103948600-103970000	Weak transcription	Aorta	Aorta
44	chr4:103951000-103956200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:103951400-103965000	Weak transcription	Fetal Brain Female	brain
46	chr4:103951400-103972400	Weak transcription	NHLF	lung
47	chr4:103951600-103957000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:103951800-103955000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr4:103952200-103956800	Weak transcription	Primary B cells from cord blood	blood
50	chr4:103952200-103956800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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