Variant report

Variant	rs3817870
Chromosome Location	chr1:209849002-209849003
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	CTCF	chr1:209848980-209849130	SK-N-SH_RA	brain:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
2	MAX	chr1:209848418-209849484	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr1:209848491-209849056	U87	brain:	n/a	n/a
4	POLR2A	chr1:209848491-209849062	U87	brain:	n/a	n/a
5	CTCF	chr1:209848880-209849030	AoAF	blood vessel:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
6	CTCF	chr1:209848900-209849050	HEK293	kidney:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
7	CTCF	chr1:209848860-209849010	GM12875	blood:	n/a	chr1:209848983-209849001 chr1:209848866-209848879 chr1:209848991-209848999
8	POLR2A	chr1:209848536-209849025	HUVEC	blood vessel:	n/a	n/a
9	CTCF	chr1:209848940-209849090	BE2_C	brain:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
10	CTCF	chr1:209848720-209849010	AG04449	skin:	n/a	chr1:209848983-209849001 chr1:209848866-209848879 chr1:209848991-209848999
11	CTBP2	chr1:209848410-209849491	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr1:209848860-209849010	Caco-2	colon:	n/a	chr1:209848983-209849001 chr1:209848866-209848879 chr1:209848991-209848999
13	CTCF	chr1:209848940-209849090	SAEC	small airway:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
14	CTCF	chr1:209848960-209849110	HCPEpiC	choroid plexus:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
15	CTCF	chr1:209848900-209849050	HPAF	blood vessel:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
16	CTCF	chr1:209848980-209849130	HMF	breast:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
17	MAX	chr1:209848334-209849646	H1-hESC	embryonic stem cell:	n/a	n/a
18	TCF12	chr1:209848125-209849142	ECC-1	luminal epithelium:	n/a	chr1:209848979-209848989
19	JUN	chr1:209845877-209850984	K562	blood:	n/a	chr1:209846829-209846839 chr1:209846830-209846838 chr1:209850154-209850163 chr1:209846657-209846666 chr1:209846828-209846840 chr1:209850457-209850468 chr1:209847133-209847144
20	UBTF	chr1:209848162-209849482	K562	blood:	n/a	n/a
21	MYC	chr1:209848350-209849184	K562	blood:	n/a	n/a
22	CTCF	chr1:209848960-209849110	AoAF	blood vessel:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
23	CTCF	chr1:209848920-209849070	SK-N-SH_RA	brain:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
24	E2F6	chr1:209848890-209849656	H1-hESC	embryonic stem cell:	n/a	chr1:209849000-209849012
25	CTCF	chr1:209848920-209849070	AG09309	skin:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
26	CTCF	chr1:209848920-209849070	HCFaa	heart:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
27	MAX	chr1:209848105-209849737	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr1:209848940-209849190	HEEpiC	esophagus:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
29	MAFK	chr1:209848215-209849006	K562	blood:	n/a	chr1:209848342-209848357
30	CTCF	chr1:209848900-209849050	AG09319	gingival:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
31	CTCF	chr1:209849000-209849150	HRE	kidney:	n/a	n/a
32	POLR2A	chr1:209845589-209851436	K562	blood:	n/a	n/a
33	CTCF	chr1:209848900-209849050	HFF	foreskin:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
34	MAX	chr1:209848257-209849079	ECC-1	luminal epithelium:	n/a	n/a
35	CTCF	chr1:209848880-209849030	AG04449	skin:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
36	ESR1	chr1:209848307-209849002	ECC-1	luminal epithelium:	n/a	chr1:209848364-209848381
37	RCOR1	chr1:209847926-209849163	K562	blood:	n/a	n/a
38	EP300	chr1:209848095-209849538	ECC-1	luminal epithelium:	n/a	chr1:209848789-209848805
39	ZNF384	chr1:209848297-209849023	K562	blood:	n/a	n/a
40	CCNT2	chr1:209848313-209849504	K562	blood:	n/a	n/a
41	CTCF	chr1:209848860-209849010	HMEC	breast:	n/a	chr1:209848983-209849001 chr1:209848866-209848879 chr1:209848991-209848999
42	CTCF	chr1:209848960-209849110	AG04450	lung:	n/a	chr1:209848983-209849001 chr1:209848991-209848999
43	BHLHE40	chr1:209848177-209849684	K562	blood:	n/a	chr1:209848854-209848870
44	MAZ	chr1:209846271-209849643	K562	blood:	n/a	chr1:209846852-209846861 chr1:209846850-209846863 chr1:209846852-209846861 chr1:209846851-209846862 chr1:209846850-209846863 chr1:209846852-209846861 chr1:209846851-209846862 chr1:209846851-209846860
45	MAX	chr1:209848047-209849006	ECC-1	luminal epithelium:	n/a	n/a
46	ZMIZ1	chr1:209848045-209849180	K562	blood:	n/a	n/a
47	NFIC	chr1:209848255-209849176	ECC-1	luminal epithelium:	n/a	n/a
48	ZNF143	chr1:209848773-209849606	H1-hESC	embryonic stem cell:	n/a	n/a
49	EP300	chr1:209848312-209849037	K562	blood:	n/a	chr1:209848789-209848805
50	MAX	chr1:209848357-209849616	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000227591	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10779511	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10779512	0.81[ASN][1000 genomes]
rs4844486	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6540546	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs932374	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3350621	chr1:209848656-209849030	Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209847000-209850000	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr1:209847400-209850000	Flanking Active TSS	Duodenum Mucosa	Duodenum
3	chr1:209847400-209850600	Flanking Active TSS	Liver	Liver
4	chr1:209847600-209849200	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
5	chr1:209847600-209849600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:209847600-209850000	Active TSS	Rectal Smooth Muscle	rectum
7	chr1:209847800-209849400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:209847800-209850200	Active TSS	Psoas Muscle	Psoas
9	chr1:209848000-209849400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:209848000-209849400	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr1:209848000-209849600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:209848000-209849600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
13	chr1:209848000-209849800	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr1:209848000-209849800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr1:209848200-209849200	Bivalent/Poised TSS	Fetal Brain Female	brain
16	chr1:209848200-209849400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr1:209848200-209849400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:209848200-209849400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
19	chr1:209848200-209849400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr1:209848200-209849400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:209848200-209849400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr1:209848200-209849400	Active TSS	Fetal Kidney	kidney
23	chr1:209848200-209849400	Flanking Active TSS	Stomach Mucosa	stomach
24	chr1:209848200-209849400	Bivalent/Poised TSS	A549	lung
25	chr1:209848200-209849400	Flanking Active TSS	HMEC	breast
26	chr1:209848200-209849600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:209848200-209849600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
28	chr1:209848200-209849600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:209848200-209849600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr1:209848200-209849600	Flanking Active TSS	Ovary	ovary
31	chr1:209848200-209849600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr1:209848200-209849800	Active TSS	Brain Cingulate Gyrus	brain
33	chr1:209848200-209849800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr1:209848400-209849200	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:209848400-209849200	Flanking Bivalent TSS/Enh	Placenta	Placenta
36	chr1:209848400-209849400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr1:209848400-209849400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:209848400-209849400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:209848400-209849400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
40	chr1:209848400-209849400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:209848400-209849400	Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr1:209848400-209849400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
43	chr1:209848400-209849400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
44	chr1:209848400-209849400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:209848400-209849400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:209848400-209849400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:209848400-209849400	Active TSS	Brain Substantia Nigra	brain
48	chr1:209848400-209849400	Flanking Active TSS	Esophagus	oesophagus
49	chr1:209848400-209849400	Flanking Active TSS	Lung	lung
50	chr1:209848400-209849600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell

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