Variant report

Variant	rs34869
Chromosome Location	chr5:115152694-115152695
allele	C/G
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	REST	chr5:115151061-115153120	H1-neurons	neurons:	n/a	chr5:115152626-115152639
2	E2F6	chr5:115151447-115152881	H1-hESC	embryonic stem cell:	n/a	chr5:115151891-115151901 chr5:115152461-115152470
3	CHD2	chr5:115151997-115152705	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr5:115152084-115152746	SK-N-MC	brain:	n/a	n/a
5	CREB1	chr5:115151688-115152885	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD1	chr5:115152141-115152996	IMR90	lung:	n/a	n/a
7	TAF7	chr5:115151989-115152833	H1-hESC	embryonic stem cell:	n/a	n/a
8	HEY1	chr5:115152060-115152846	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:115152019-115152848	SK-N-MC	brain:	n/a	n/a
10	TAF1	chr5:115151897-115152873	H1-neurons	neurons:	n/a	n/a
11	JUND	chr5:115151296-115152876	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr5:115151132-115152960	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr5:115151975-115152804	H1-hESC	embryonic stem cell:	n/a	n/a
14	JUND	chr5:115151780-115152752	H1-hESC	embryonic stem cell:	n/a	n/a
15	YY1	chr5:115151599-115152915	H1-hESC	embryonic stem cell:	n/a	chr5:115151779-115151790 chr5:115152458-115152467 chr5:115151884-115151898 chr5:115151889-115151898
16	ZNF143	chr5:115152141-115152737	H1-hESC	embryonic stem cell:	n/a	n/a
17	YY1	chr5:115151796-115152846	H1-hESC	embryonic stem cell:	n/a	chr5:115152458-115152467 chr5:115151884-115151898 chr5:115151889-115151898
18	EP300	chr5:115152206-115152767	H1-hESC	embryonic stem cell:	n/a	chr5:115152721-115152735
19	TAF1	chr5:115152021-115152880	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZNF263	chr5:115150963-115152852	HEK293-T-REx	kidney:	n/a	n/a
21	POLR2A	chr5:115152027-115152844	HepG2	liver:	n/a	n/a
22	POLR2A	chr5:115152135-115152697	IMR90	lung:	n/a	n/a
23	POLR2A	chr5:115151190-115152887	H1-neurons	neurons:	n/a	n/a
24	POLR2A	chr5:115151822-115152891	HepG2	liver:	n/a	n/a
25	POLR2A	chr5:115152157-115152710	HepG2	liver:	n/a	n/a
26	POLR2A	chr5:115151205-115152841	H1-hESC	embryonic stem cell:	n/a	n/a
27	BHLHE40	chr5:115151693-115152773	HepG2	liver:	n/a	n/a
28	POLR2A	chr5:115152598-115152820	HepG2	liver:	n/a	n/a
29	POLR2A	chr5:115151741-115152866	H1-hESC	embryonic stem cell:	n/a	n/a
30	TAF1	chr5:115151486-115152833	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr5:115151831-115152733	H1-hESC	embryonic stem cell:	n/a	n/a
32	REST	chr5:115151989-115152775	H1-neurons	neurons:	n/a	chr5:115152626-115152639
33	YY1	chr5:115152576-115152820	SK-N-SH_RA	brain:	n/a	n/a
34	POLR2A	chr5:115151709-115152864	H1-hESC	embryonic stem cell:	n/a	n/a
35	BRCA1	chr5:115152301-115152809	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr5:115152563-115152773	HepG2	liver:	n/a	n/a
37	GATA2	chr5:115151802-115152832	SH-SY5Y	brain:	n/a	chr5:115152723-115152733
38	TAF1	chr5:115151500-115152950	H1-neurons	neurons:	n/a	n/a
39	MAX	chr5:115151322-115152818	H1-hESC	embryonic stem cell:	n/a	chr5:115151855-115151864
40	POLR2A	chr5:115152571-115152819	SK-N-SH	brain:	n/a	n/a
41	CREB1	chr5:115151989-115152956	H1-hESC	embryonic stem cell:	n/a	n/a
42	TBP	chr5:115152098-115152850	HepG2	liver:	n/a	n/a
43	E2F6	chr5:115152219-115152761	H1-hESC	embryonic stem cell:	n/a	chr5:115152461-115152470
44	CHD1	chr5:115151626-115152863	H1-hESC	embryonic stem cell:	n/a	chr5:115151795-115151805
45	YY1	chr5:115152466-115152816	SK-N-SH_RA	brain:	n/a	n/a
46	TBP	chr5:115151462-115152838	H1-hESC	embryonic stem cell:	n/a	n/a
47	BACH1	chr5:115151790-115152797	H1-hESC	embryonic stem cell:	n/a	n/a
48	SIN3A	chr5:115151138-115152731	H1-hESC	embryonic stem cell:	n/a	chr5:115151909-115151920

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115147173..115150653-chr5:115151450..115154733,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AP3S1-1	chr5:115151929-115152868	NONHSAT103327

Variant related genes	Relation type
CDO1	TF binding region
ENSG00000129596	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10434761	0.95[ASN][1000 genomes]
rs1058600	0.95[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs12189155	0.84[ASN][1000 genomes]
rs12520248	0.95[ASN][1000 genomes]
rs12521324	0.87[ASN][1000 genomes]
rs13174348	0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs154757	0.93[ASN][1000 genomes]
rs154759	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs258738	0.81[ASN][1000 genomes]
rs26531	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs26533	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs26534	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs26535	0.89[ASN][1000 genomes]
rs26536	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs26537	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs34850	0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs34851	0.95[ASN][1000 genomes]
rs34852	0.96[ASN][1000 genomes]
rs35053218	0.91[ASN][1000 genomes]
rs35179959	0.92[ASN][1000 genomes]
rs35903246	0.90[ASN][1000 genomes]
rs3797570	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.91[ASN][1000 genomes]
rs40095	0.96[ASN][1000 genomes]
rs4920892	0.82[ASN][1000 genomes]
rs57633641	0.91[ASN][1000 genomes]
rs6594906	0.91[ASN][1000 genomes]
rs6872406	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6880889	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs71581214	0.81[ASN][1000 genomes]
rs7726368	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34869	CDO1	cis	Thyroid	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115149200-115152800	Active TSS	Aorta	Aorta
2	chr5:115149800-115153000	Active TSS	Liver	Liver
3	chr5:115150600-115153000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr5:115150800-115152800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:115150800-115152800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:115150800-115152800	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr5:115150800-115153400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr5:115151000-115152800	Active TSS	H9 Cell Line	embryonic stem cell
9	chr5:115151000-115152800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr5:115151000-115152800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:115151000-115152800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:115151000-115152800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
13	chr5:115151000-115153000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:115151000-115153200	Active TSS	Fetal Brain Male	brain
15	chr5:115151000-115153200	Active TSS	Fetal Brain Female	brain
16	chr5:115151000-115153200	Active TSS	Fetal Kidney	kidney
17	chr5:115151200-115152800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:115151200-115152800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:115151200-115152800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
20	chr5:115151200-115153000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
21	chr5:115151200-115153000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
22	chr5:115151200-115153000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
23	chr5:115151200-115153000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
24	chr5:115151200-115153200	Active TSS	Brain Germinal Matrix	brain
25	chr5:115151200-115153200	Bivalent/Poised TSS	Fetal Lung	lung
26	chr5:115151400-115152800	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:115151400-115152800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:115151400-115152800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
29	chr5:115151400-115152800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:115151400-115152800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:115151400-115152800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:115151400-115152800	Active TSS	Brain Angular Gyrus	brain
33	chr5:115151400-115152800	Active TSS	Brain Hippocampus Middle	brain
34	chr5:115151400-115152800	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr5:115151400-115152800	Active TSS	Brain Substantia Nigra	brain
36	chr5:115151400-115152800	Flanking Active TSS	Lung	lung
37	chr5:115151400-115152800	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
38	chr5:115151400-115152800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
39	chr5:115151400-115152800	Flanking Bivalent TSS/Enh	HMEC	breast
40	chr5:115151400-115152800	Bivalent/Poised TSS	HSMM	muscle
41	chr5:115151400-115152800	Bivalent/Poised TSS	HSMMtube	muscle
42	chr5:115151400-115152800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
43	chr5:115151400-115153000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:115151400-115153000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
45	chr5:115151400-115153000	Active TSS	Ovary	ovary
46	chr5:115151600-115152800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr5:115151600-115152800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
48	chr5:115151600-115152800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr5:115151600-115152800	Flanking Active TSS	Right Ventricle	heart
50	chr5:115151600-115152800	Bivalent/Poised TSS	Thymus	Thymus

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