Variant report

Variant	rs2001209
Chromosome Location	chr3:23962646-23962647
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:155)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:155 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:23962628-23962948	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:23962331-23963991	GM12878	blood:	n/a	n/a
3	JUND	chr3:23962361-23963233	HCT-116	colon:	n/a	n/a
4	PML	chr3:23961122-23963134	K562	blood:	n/a	n/a
5	HEY1	chr3:23962552-23963011	K562	blood:	n/a	n/a
6	POLR2A	chr3:23961148-23964111	MCF10A-Er-Src	breast:	n/a	n/a
7	BCL3	chr3:23962610-23962939	GM12878	blood:	n/a	n/a
8	ATF3	chr3:23962413-23963202	A549	lung:	n/a	n/a
9	POLR2A	chr3:23961138-23963839	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr3:23958045-23963842	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:23962391-23963246	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:23961371-23963855	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr3:23961180-23964553	GM12891	blood:	n/a	n/a
14	BRCA1	chr3:23962641-23962886	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr3:23961503-23963863	K562	blood:	n/a	n/a
16	HEY1	chr3:23962405-23962904	K562	blood:	n/a	n/a
17	POLR2A	chr3:23961166-23963865	GM12878	blood:	n/a	n/a
18	GTF2F1	chr3:23962339-23962973	K562	blood:	n/a	n/a
19	MBD4	chr3:23961405-23963188	HepG2	liver:	n/a	n/a
20	POLR2A	chr3:23962618-23962890	GM12878	blood:	n/a	n/a
21	NFATC1	chr3:23961447-23963282	GM12878	blood:	n/a	n/a
22	TRIM28	chr3:23962392-23963075	K562	blood:	n/a	n/a
23	MAFF	chr3:23962579-23962923	K562	blood:	n/a	n/a
24	POLR2A	chr3:23957976-23965870	K562	blood:	n/a	n/a
25	POLR2A	chr3:23962487-23962825	A549	lung:	n/a	n/a
26	POLR2A	chr3:23957870-23963941	H1-hESC	embryonic stem cell:	n/a	n/a
27	PML	chr3:23961388-23963850	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:23961064-23963934	K562	blood:	n/a	n/a
29	ATF2	chr3:23961592-23963025	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:23962297-23963127	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr3:23962407-23963751	NB4	blood:	n/a	n/a
32	POLR2A	chr3:23961218-23963277	HL-60	blood:	n/a	n/a
33	GATA3	chr3:23961846-23963079	A549	lung:	n/a	n/a
34	PBX3	chr3:23962469-23963073	A549	lung:	n/a	n/a
35	NFIC	chr3:23962569-23963217	GM12878	blood:	n/a	chr3:23962665-23962682
36	POLR2A	chr3:23962275-23964028	H1-hESC	embryonic stem cell:	n/a	n/a
37	ATF2	chr3:23961107-23963189	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr3:23961309-23963207	PBDE	blood:	n/a	n/a
39	ATF2	chr3:23962388-23963029	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr3:23961267-23963083	HepG2	liver:	n/a	n/a
41	POLR2A	chr3:23961272-23963810	GM18951	blood:	n/a	n/a
42	POLR2A	chr3:23961184-23963270	HCT-116	colon:	n/a	n/a
43	ELF1	chr3:23962433-23962864	A549	lung:	n/a	n/a
44	ARID3A	chr3:23962295-23963033	K562	blood:	n/a	n/a
45	POLR2A	chr3:23960818-23964110	MCF-7	breast:	n/a	n/a
46	SP4	chr3:23962608-23963100	H1-hESC	embryonic stem cell:	n/a	n/a
47	TEAD4	chr3:23962331-23963037	K562	blood:	n/a	n/a
48	POLR2A	chr3:23961089-23963277	U87	brain:	n/a	n/a
49	POLR2A	chr3:23961251-23963895	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr3:23960446-23964170	HepG2	liver:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:23960526..23962863-chr3:24013920..24016141,2	K562	blood:
2	chr3:23961452..23965156-chr3:23999587..24004253,5	MCF-7	breast:
3	chr3:23961179..23963059-chr3:24534695..24537090,2	K562	blood:
4	chr3:23931925..23934532-chr3:23961376..23962926,2	MCF-7	breast:
5	chr3:23748425..23751412-chr3:23960441..23962908,2	K562	blood:
6	chr3:23960922..23962761-chr3:24002838..24004607,2	K562	blood:
7	chr3:23905396..23907030-chr3:23960105..23962888,2	K562	blood:
8	chr3:23961544..23965594-chr3:24039129..24042717,4	K562	blood:
9	chr3:23928269..23930887-chr3:23960946..23963532,2	MCF-7	breast:
10	chr3:23926182..23928308-chr3:23961737..23963775,2	MCF-7	breast:
11	chr3:23846543..23848626-chr3:23961090..23963497,2	K562	blood:
12	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
13	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
14	chr3:23960325..23963916-chr3:24723703..24727555,4	MCF-7	breast:

No data

Variant related genes	Relation type
NKIRAS1	TF binding region
ENSG00000151090	Chromatin interaction
ENSG00000228791	Chromatin interaction
ENSG00000170142	Chromatin interaction
ENSG00000223791	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000174738	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10865790	0.85[MEX][hapmap]
rs1135452	0.95[ASN][1000 genomes]
rs11922609	0.81[CHD][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs28522849	0.85[EUR][1000 genomes]
rs35886023	0.86[EUR][1000 genomes]
rs4619736	0.91[ASN][1000 genomes]
rs5001573	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62253383	0.87[EUR][1000 genomes]
rs6773828	0.95[ASN][1000 genomes]
rs6778970	0.81[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs6800407	0.81[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs72627066	0.93[ASN][1000 genomes]
rs7633520	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637968	0.81[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap]
rs9755750	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851068	0.81[MEX][hapmap]
rs9862416	0.95[ASN][1000 genomes]
rs9863605	0.95[CEU][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2001209	NR1D2	cis	lymphoblastoid	seeQTL
rs2001209	NR1D2	cis	Cerebellum	GTEx
rs2001209	NR1D2	cis	Frontal Cortex	GTEx
rs2001209	NR1D2	cis	parietal	SCAN
rs2001209	NR1D2	cis	Lymphoblastoid	GTEx
rs2001209	NR1D2	cis	Brain Pons	GTEx
rs2001209	NKIRAS1	Cis_1M	lymphoblastoid	RTeQTL
rs2001209	NR1D2	Cis_1M	lymphoblastoid	RTeQTL
rs2001209	ZNF385D	cis	parietal	SCAN
rs2001209	NR1D2	cis	Temporal Cortex	GTEx
rs2001209	NKIRAS1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23959600-23965200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:23959600-23965600	Weak transcription	Spleen	Spleen
3	chr3:23959600-23969400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:23959800-23965000	Weak transcription	Ovary	ovary
5	chr3:23960000-23965000	Weak transcription	Colonic Mucosa	Colon
6	chr3:23960200-23963000	Genic enhancers	Primary B cells from cord blood	blood
7	chr3:23960200-23964400	Strong transcription	Placenta	Placenta
8	chr3:23960200-23967000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:23960200-23969400	Weak transcription	Esophagus	oesophagus
10	chr3:23960400-23963600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:23960400-23963800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:23960400-23963800	Strong transcription	Brain Hippocampus Middle	brain
13	chr3:23960400-23963800	Strong transcription	Thymus	Thymus
14	chr3:23960400-23964200	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:23960400-23964600	Strong transcription	Fetal Muscle Leg	muscle
16	chr3:23960600-23963000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr3:23960600-23963200	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:23960600-23963600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr3:23960600-23963800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr3:23960600-23963800	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:23960600-23964000	Strong transcription	Liver	Liver
22	chr3:23960600-23964400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:23960600-23964800	Strong transcription	Brain Germinal Matrix	brain
24	chr3:23960600-23965000	Strong transcription	Fetal Stomach	stomach
25	chr3:23960800-23962800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:23960800-23963000	Strong transcription	HSMM	muscle
27	chr3:23960800-23963600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr3:23960800-23963800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:23960800-23963800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr3:23960800-23963800	Strong transcription	Adipose Nuclei	Adipose
31	chr3:23960800-23963800	Strong transcription	Brain Anterior Caudate	brain
32	chr3:23960800-23963800	Strong transcription	Left Ventricle	heart
33	chr3:23960800-23964000	Strong transcription	Fetal Thymus	thymus
34	chr3:23960800-23964200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:23960800-23965000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr3:23961000-23963000	Weak transcription	Fetal Intestine Small	intestine
37	chr3:23961000-23964600	Strong transcription	Fetal Muscle Trunk	muscle
38	chr3:23961000-23966600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:23961200-23963800	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:23961400-23963600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:23961400-23963600	Strong transcription	Brain Angular Gyrus	brain
42	chr3:23961400-23964000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:23961400-23964000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr3:23961400-23966000	Strong transcription	Stomach Smooth Muscle	stomach
45	chr3:23961600-23962800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:23961600-23963800	Strong transcription	Aorta	Aorta
47	chr3:23961600-23963800	Strong transcription	Right Ventricle	heart
48	chr3:23961600-23964600	Strong transcription	Lung	lung
49	chr3:23961800-23962800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:23961800-23963000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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