Variant report

Variant	rs6596858
Chromosome Location	chr6:1871901-1871902
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10484693	0.82[MEX][hapmap]
rs13190775	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13197177	0.87[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs13204935	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1998519	0.88[GIH][hapmap];0.92[EUR][1000 genomes]
rs35946812	0.96[EUR][1000 genomes]
rs3778536	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3778554	0.86[CHB][hapmap]
rs3800086	0.81[JPT][hapmap];0.84[TSI][hapmap]
rs3800090	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3800105	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3823279	0.87[CEU][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.92[EUR][1000 genomes]
rs57347378	0.96[EUR][1000 genomes]
rs6912444	0.81[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7764600	0.86[CHB][hapmap]
rs9503028	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9503031	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9503043	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv538094	chr6:1757776-1907505	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
9	nsv883383	chr6:1775436-1918572	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv883384	chr6:1787862-1942538	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1019895	chr6:1832936-1882435	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1032149	chr6:1848148-2006021	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv883385	chr6:1869592-1915828	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6596858	C8orf58	cis	Liver	GTEx
rs6596858	C8orf58	trans	multi-tissue	Pritchard

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1842800-1872400	Weak transcription	Gastric	stomach
2	chr6:1851200-1895600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:1851400-1872200	Weak transcription	Pancreas	Pancrea
4	chr6:1851400-1909600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:1857600-1877200	Weak transcription	Primary T cells from cord blood	blood
6	chr6:1865200-1884600	Weak transcription	Small Intestine	intestine
7	chr6:1865800-1872200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:1866600-1872000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:1867000-1872000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:1867000-1873800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:1867200-1872200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:1868000-1873600	Weak transcription	Stomach Mucosa	stomach
13	chr6:1869200-1872400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:1869200-1874000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr6:1869200-1874200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr6:1869200-1874200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr6:1869400-1873400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr6:1869400-1873800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr6:1869400-1873800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr6:1869400-1874200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr6:1869400-1874400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr6:1869600-1873800	Enhancers	H9 Cell Line	embryonic stem cell
23	chr6:1870400-1872200	Weak transcription	Brain Anterior Caudate	brain
24	chr6:1870400-1872200	Weak transcription	Ovary	ovary
25	chr6:1870600-1873600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:1870600-1874000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:1870600-1874200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:1870800-1872000	Weak transcription	Aorta	Aorta
29	chr6:1870800-1872000	Weak transcription	HSMMtube	muscle
30	chr6:1870800-1874200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:1871000-1874200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:1871000-1895400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:1871200-1873800	Weak transcription	HepG2	liver
34	chr6:1871200-1874200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:1871200-1874200	Enhancers	Fetal Kidney	kidney
36	chr6:1871400-1872800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr6:1871400-1873200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:1871400-1873200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:1871400-1873200	Enhancers	Fetal Lung	lung
40	chr6:1871400-1876600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:1871600-1872200	Enhancers	Brain Hippocampus Middle	brain
42	chr6:1871600-1872600	Weak transcription	Fetal Intestine Small	intestine
43	chr6:1871600-1874400	Enhancers	Fetal Muscle Leg	muscle
44	chr6:1871800-1872000	Enhancers	Brain Cingulate Gyrus	brain
45	chr6:1871800-1872000	Enhancers	Brain Substantia Nigra	brain
46	chr6:1871800-1873200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:1871800-1874000	Enhancers	Cortex derived primary cultured neurospheres	brain

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