Variant report

Variant	rs6558536
Chromosome Location	chr8:1720204-1720205
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	chr8:1719958-1720723	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:1717537..1720996-chr8:1730538..1734244,3	K562	blood:

Variant related genes	Relation type
CLN8	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10097891	0.82[ASN][1000 genomes]
rs10100341	0.82[ASN][1000 genomes]
rs11778824	0.82[AMR][1000 genomes]
rs13256424	0.82[ASN][1000 genomes]
rs4875806	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4875957	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6982516	0.83[AMR][1000 genomes]
rs6991773	0.82[ASN][1000 genomes]
rs6991783	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6993706	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7008465	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7014327	0.82[ASN][1000 genomes]
rs7014823	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7015858	0.82[ASN][1000 genomes]
rs7341635	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889697	chr8:1238564-1861971	Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1031375	chr8:1320657-1722050	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv889704	chr8:1563904-1965389	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv889707	chr8:1581839-1920461	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv889708	chr8:1581839-1965389	Genic enhancers Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv889709	chr8:1581839-1965389	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv889711	chr8:1591412-1904157	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv889712	chr8:1591412-2337777	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv889714	chr8:1616718-1965389	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv934075	chr8:1626857-1736355	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1034490	chr8:1654716-1782467	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
12	nsv609527	chr8:1681733-1753497	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
13	nsv870096	chr8:1682851-1767342	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
14	nsv465274	chr8:1685064-1728292	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv609528	chr8:1685064-1728292	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv532892	chr8:1687433-1839578	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
17	esv2755149	chr8:1689290-1755281	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
18	nsv465275	chr8:1697086-1768004	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
19	nsv609529	chr8:1697086-1768004	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
20	nsv465276	chr8:1701432-1777571	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
21	nsv609530	chr8:1701432-1777571	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
22	nsv609531	chr8:1717036-1965389	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
23	nsv932825	chr8:1719042-1736355	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6558536	CTD-2336O2.1	cis	Adipose Subcutaneous	GTEx
rs6558536	CTD-2336O2.1	cis	Esophagus Muscularis	GTEx
rs6558536	CTD-2336O2.1	cis	Nerve Tibial	GTEx
rs6558536	CTD-2336O2.1	cis	lung	GTEx
rs6558536	CTD-2336O2.1	cis	Muscle Skeletal	GTEx
rs6558536	CTD-2336O2.1	cis	Artery Tibial	GTEx
rs6558536	CTD-2336O2.1	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:1713400-1721000	Weak transcription	Psoas Muscle	Psoas
2	chr8:1713400-1727000	Weak transcription	NHDF-Ad	bronchial
3	chr8:1713400-1735800	Weak transcription	Fetal Brain Male	brain
4	chr8:1713600-1721400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr8:1713600-1729600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr8:1714000-1728000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr8:1714000-1729800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr8:1714400-1729200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr8:1714800-1727000	Strong transcription	Fetal Intestine Small	intestine
10	chr8:1715400-1726800	Strong transcription	Fetal Stomach	stomach
11	chr8:1715400-1727800	Weak transcription	Small Intestine	intestine
12	chr8:1715400-1729200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr8:1715600-1725600	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr8:1716400-1726800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr8:1716600-1723000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr8:1716600-1725200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr8:1716600-1727000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr8:1716800-1721000	Strong transcription	Liver	Liver
19	chr8:1716800-1721200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr8:1716800-1722000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr8:1717000-1724600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr8:1717000-1724600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr8:1717200-1722400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr8:1717400-1728400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr8:1717600-1721000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr8:1717600-1721000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr8:1717600-1722000	Weak transcription	HSMMtube	muscle
28	chr8:1717600-1724600	Strong transcription	HMEC	breast
29	chr8:1717600-1726400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr8:1717600-1731000	Weak transcription	Fetal Lung	lung
31	chr8:1717800-1722400	Strong transcription	NHEK	skin
32	chr8:1717800-1724600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr8:1717800-1725000	Weak transcription	HSMM	muscle
34	chr8:1717800-1725200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr8:1717800-1726200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr8:1717800-1726200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr8:1717800-1727800	Weak transcription	Stomach Mucosa	stomach
38	chr8:1718000-1720600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr8:1718000-1721000	Weak transcription	Hela-S3	cervix
40	chr8:1718000-1721200	Weak transcription	Right Atrium	heart
41	chr8:1718000-1722000	Strong transcription	HepG2	liver
42	chr8:1718000-1722400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr8:1718000-1726000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr8:1718000-1726600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr8:1718000-1727800	Weak transcription	Fetal Kidney	kidney
46	chr8:1718000-1728000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr8:1718000-1732400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr8:1718000-1732800	Weak transcription	Fetal Heart	heart
49	chr8:1718000-1736000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr8:1718200-1720800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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