Variant report

Variant	rs3753897
Chromosome Location	chr1:165414511-165414512
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr1:165414198-165414702	SH-SY5Y	brain:	n/a	n/a
2	CREB1	chr1:165414132-165414614	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:165414113-165414629	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr1:165414114-165414638	H1-neurons	neurons:	n/a	n/a
5	SIN3A	chr1:165414176-165414841	H1-hESC	embryonic stem cell:	n/a	chr1:165414504-165414513

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:165414491-165414541	HUVEC	blood vessel:	n/a
2	chr1:165414491-165414541	GM12878	blood:	n/a
3	chr1:165414491-165414541	HCF	heart:	n/a
4	chr1:165414491-165414541	HAEpiC	amniotic membrane:	n/a
5	chr1:165414491-165414541	NB4	blood:	n/a
6	chr1:165414491-165414541	PFSK-1	brain:	n/a
7	chr1:165414491-165414541	PANC-1	pancreas:	n/a
8	chr1:165414491-165414541	GM12892	blood:	n/a
9	chr1:165414491-165414541	NHBE	bronchial:	n/a
10	chr1:165414491-165414541	MCF-7	breast:	n/a
11	chr1:165414491-165414541	HNPCEpiC	eye:	n/a
12	chr1:165414491-165414541	BJ	skin:	n/a
13	chr1:165414491-165414541	HCM	heart:	n/a
14	chr1:165414491-165414541	PrEC	prostate:	n/a
15	chr1:165414491-165414541	H1-hESC	embryonic stem cell:	embryo
16	chr1:165414491-165414541	T-47D	breast:	n/a
17	chr1:165414491-165414541	U87	brain:	n/a
18	chr1:165414491-165414541	K562	blood:	n/a
19	chr1:165414491-165414541	HIPEpiC	eye:	n/a
20	chr1:165414491-165414541	MCF10A-Er-Src	breast:	n/a
21	chr1:165414491-165414541	NH-A	brain:	n/a
22	chr1:165414491-165414541	LNCaP	prostate:	n/a
23	chr1:165414491-165414541	A549	lung:	n/a
24	chr1:165414491-165414541	AoSMC	blood vessel:	n/a
25	chr1:165414491-165414541	Hepatocyte	liver:	n/a
26	chr1:165414491-165414541	ECC-1	luminal epithelium:	n/a
27	chr1:165414491-165414541	BE2_C	brain:	n/a
28	chr1:165414491-165414541	GM19239	blood:	n/a
29	chr1:165414491-165414541	CMK	blood:	n/a
30	chr1:165414491-165414541	SK-N-SH	brain:	n/a
31	chr1:165414491-165414541	AG09319	gingival:	n/a
32	chr1:165414491-165414541	HepG2	liver:	n/a
33	chr1:165414491-165414541	AG04449	skin:	fetal
34	chr1:165414491-165414541	AG10803	skin:	n/a
35	chr1:165414491-165414541	AG04450	lung:	fetal
36	chr1:165414491-165414541	AG09309	skin:	n/a
37	chr1:165414491-165414541	HCPEpiC	choroid plexus:	n/a
38	chr1:165414491-165414541	HRCEpiC	kidney:	n/a
39	chr1:165414491-165414541	SKMC	muscle:	n/a
40	chr1:165414491-165414541	NT2-D1	testis:	n/a
41	chr1:165414491-165414541	HL-60	blood:	n/a
42	chr1:165414491-165414541	HRPEpiC	eye:	n/a
43	chr1:165414491-165414541	RPTEC	kidney:	n/a
44	chr1:165414491-165414541	HCT-116	colon:	n/a
45	chr1:165414491-165414541	Hela-S3	cervix:	n/a
46	chr1:165414491-165414541	IMR90	lung:	fetal
47	chr1:165414491-165414541	SK-N-SH_RA	brain:	n/a
48	chr1:165414491-165414541	Jurkat	blood:	n/a
49	chr1:165414491-165414541	HEK293	kidney:	embryo
50	chr1:165414491-165414541	GM06990	blood:	n/a

No data

Variant related genes	Relation type
RXRG	TF binding region
RXRG	CpG island

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12401512	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12402931	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12411116	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16844995	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16845022	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3753898	0.86[EUR][1000 genomes]
rs58323504	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6671584	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73022924	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73022927	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165412200-165414800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:165412400-165414800	Active TSS	Brain Anterior Caudate	brain
3	chr1:165412800-165414600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
4	chr1:165412800-165414800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:165412800-165414800	Active TSS	Brain Substantia Nigra	brain
6	chr1:165413000-165414800	Active TSS	Brain Angular Gyrus	brain
7	chr1:165413200-165414600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:165413200-165414600	Enhancers	Placenta	Placenta
9	chr1:165413200-165414800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:165413200-165414800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
11	chr1:165413200-165414800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:165413400-165414600	Active TSS	Psoas Muscle	Psoas
13	chr1:165413400-165414800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr1:165413400-165414800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:165413400-165414800	Active TSS	Brain Cingulate Gyrus	brain
16	chr1:165413600-165414600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
17	chr1:165413800-165414600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:165413800-165414600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
19	chr1:165413800-165414600	Active TSS	Lung	lung
20	chr1:165413800-165414800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:165413800-165414800	Bivalent/Poised TSS	Colonic Mucosa	Colon
22	chr1:165413800-165415000	Enhancers	Spleen	Spleen
23	chr1:165414000-165414600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr1:165414000-165414600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
25	chr1:165414000-165414600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:165414000-165414600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:165414000-165414600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:165414000-165414600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:165414000-165414600	Enhancers	Gastric	stomach
30	chr1:165414000-165414600	Active TSS	Rectal Smooth Muscle	rectum
31	chr1:165414000-165414800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
32	chr1:165414000-165414800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
33	chr1:165414000-165414800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
34	chr1:165414000-165414800	Active TSS	Fetal Kidney	kidney
35	chr1:165414000-165414800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
36	chr1:165414000-165414800	Bivalent/Poised TSS	NHEK	skin
37	chr1:165414000-165415200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:165414200-165414600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:165414200-165414600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:165414200-165414600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:165414200-165414600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
42	chr1:165414200-165414600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr1:165414200-165414600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:165414200-165414600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:165414200-165414600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:165414200-165414600	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
47	chr1:165414200-165414600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
48	chr1:165414200-165414600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
49	chr1:165414200-165414600	Active TSS	Aorta	Aorta
50	chr1:165414200-165414600	Enhancers	Esophagus	oesophagus

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