Variant report

Variant	rs6855978
Chromosome Location	chr4:119555093-119555094
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12651650	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34016523	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34766719	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35183273	0.98[ASN][1000 genomes]
rs35731099	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4001330	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67276048	0.95[ASN][1000 genomes]
rs67655207	0.97[ASN][1000 genomes]
rs6833597	0.98[ASN][1000 genomes]
rs71241793	0.95[ASN][1000 genomes]
rs71610209	0.82[AMR][1000 genomes]
rs71610221	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9760578	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1002771	chr4:119125361-119571237	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv427693	chr4:119493919-119674742	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv980251	chr4:119510579-119563981	Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1824927	chr4:119521936-119577466	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv966369	chr4:119539088-119559938	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv1822873	chr4:119542500-119577466	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv16226	chr4:119552399-119584340	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6855978	RP11-384K6.6	cis	Esophagus Mucosa	GTEx
rs6855978	RP11-384K6.2	cis	Whole Blood	GTEx
rs6855978	RP11-384K6.2	cis	Artery Tibial	GTEx
rs6855978	RP11-384K6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs6855978	RP11-384K6.2	cis	Thyroid	GTEx
rs6855978	RP11-384K6.6	cis	Nerve Tibial	GTEx
rs6855978	RP11-384K6.6	cis	Artery Tibial	GTEx
rs6855978	RP11-384K6.2	cis	Adipose Subcutaneous	GTEx
rs6855978	RP11-384K6.6	cis	Thyroid	GTEx
rs6855978	RP11-384K6.6	cis	Adipose Subcutaneous	GTEx
rs6855978	RP11-384K6.2	cis	Nerve Tibial	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119513400-119557200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr4:119513600-119555800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:119513600-119559200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:119513800-119556000	Weak transcription	Fetal Lung	lung
5	chr4:119518800-119557000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr4:119519800-119559000	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:119526000-119556200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:119527800-119555800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr4:119528800-119558000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr4:119538600-119555200	Weak transcription	Brain Germinal Matrix	brain
11	chr4:119542000-119557200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr4:119547400-119555600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:119549000-119556000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:119549200-119555800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:119549200-119555800	Strong transcription	Spleen	Spleen
16	chr4:119549200-119557800	Strong transcription	Fetal Stomach	stomach
17	chr4:119549400-119556600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:119549600-119557600	Strong transcription	Fetal Intestine Small	intestine
19	chr4:119550000-119555800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:119550200-119555600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:119550200-119555800	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr4:119550200-119555800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr4:119550200-119556800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:119550400-119556000	Strong transcription	Gastric	stomach
25	chr4:119550400-119559000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:119550600-119555800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr4:119551200-119555400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:119551200-119555600	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr4:119551200-119557200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:119551200-119557800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:119551400-119557200	Weak transcription	NHLF	lung
32	chr4:119551600-119556800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:119551600-119557800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:119552200-119555800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:119552200-119555800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:119552400-119555200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:119552400-119555400	Strong transcription	Right Ventricle	heart
38	chr4:119552400-119555800	Strong transcription	Lung	lung
39	chr4:119552800-119555600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:119553000-119555200	Weak transcription	Fetal Intestine Large	intestine
41	chr4:119553000-119555800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr4:119553000-119556000	Strong transcription	Placenta	Placenta
43	chr4:119553000-119557000	Weak transcription	Brain Substantia Nigra	brain
44	chr4:119553000-119557200	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr4:119553200-119555800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr4:119553200-119555800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:119553200-119557000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr4:119553200-119557000	Weak transcription	Brain Anterior Caudate	brain
49	chr4:119553200-119557200	Weak transcription	Aorta	Aorta
50	chr4:119553200-119557200	Weak transcription	Esophagus	oesophagus

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