Variant report

Variant	rs1426966
Chromosome Location	chr3:140796207-140796208
allele	A/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	EGR1	chr3:140796099-140796297	K562	blood:	n/a	n/a
2	POLR2A	chr3:140795815-140796527	H1-neurons	neurons:	n/a	n/a
3	CTCF	chr3:140796200-140796350	HBMEC	blood vessel:	n/a	chr3:140796259-140796272
4	KAP1	chr3:140795127-140796457	HEK293	kidney:	n/a	n/a
5	TCF7L2	chr3:140795510-140796479	HEK293	kidney:	n/a	n/a
6	KAP1	chr3:140795275-140796480	U2OS	brain:	n/a	n/a
7	POLR2A	chr3:140795663-140796571	H1-neurons	neurons:	n/a	n/a
8	CTCF	chr3:140796120-140796270	HBMEC	blood vessel:	n/a	n/a
9	CTCF	chr3:140796100-140796250	HPAF	blood vessel:	n/a	n/a
10	REST	chr3:140795478-140796579	H1-neurons	neurons:	n/a	chr3:140795537-140795550 chr3:140796464-140796473
11	FOXP2	chr3:140795598-140796348	SK-N-MC	brain:	n/a	n/a
12	CTCF	chr3:140796060-140796210	HCPEpiC	choroid plexus:	n/a	n/a
13	REST	chr3:140795765-140796506	H1-neurons	neurons:	n/a	chr3:140796464-140796473

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC25A36-3	chr3:140795802-140796254	NONHSAT092412

Variant related genes	Relation type
SPSB4	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1426965	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16851040	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16851042	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851043	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16851045	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16851047	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57086788	1.00[EUR][1000 genomes]
rs57164953	1.00[EUR][1000 genomes]
rs60787216	1.00[EUR][1000 genomes]
rs61201233	0.86[ASN][1000 genomes]
rs6439978	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6774862	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775066	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6777560	1.00[EUR][1000 genomes]
rs6798242	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72978075	0.86[ASN][1000 genomes]
rs72980158	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72980166	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72980168	1.00[EUR][1000 genomes]
rs72980172	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7623980	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624238	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624581	1.00[EUR][1000 genomes]

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140788200-140797200	Enhancers	H9 Cell Line	embryonic stem cell
2	chr3:140789000-140797600	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr3:140789600-140798000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:140790600-140802800	Weak transcription	Dnd41	blood
5	chr3:140791200-140796400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:140791800-140797400	Enhancers	H1 Cell Line	embryonic stem cell
7	chr3:140792000-140797400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:140792200-140797400	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr3:140792400-140797400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:140792400-140797800	Enhancers	Pancreas	Pancrea
11	chr3:140792600-140797800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:140792800-140808400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:140793400-140806600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:140793800-140797800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr3:140794000-140797400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:140794000-140797800	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr3:140794000-140813000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:140794200-140797800	Enhancers	Placenta	Placenta
19	chr3:140794800-140800600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:140795000-140796400	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr3:140795000-140796400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:140795000-140796600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr3:140795000-140796600	Enhancers	Stomach Mucosa	stomach
24	chr3:140795000-140796800	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr3:140795000-140796800	Flanking Active TSS	HSMMtube	muscle
26	chr3:140795000-140797000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:140795000-140797200	Enhancers	Fetal Brain Male	brain
28	chr3:140795000-140797200	Enhancers	Fetal Intestine Large	intestine
29	chr3:140795000-140797400	Enhancers	Lung	lung
30	chr3:140795200-140796400	Flanking Active TSS	Brain Substantia Nigra	brain
31	chr3:140795200-140796400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr3:140795200-140796600	Flanking Active TSS	Brain Cingulate Gyrus	brain
33	chr3:140795200-140796600	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr3:140795200-140797000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:140795400-140796400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:140795400-140796400	Flanking Active TSS	Fetal Lung	lung
37	chr3:140795400-140796400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr3:140795400-140796600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr3:140795400-140796600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
40	chr3:140795400-140796600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:140795400-140796600	Flanking Active TSS	Fetal Brain Female	brain
42	chr3:140795400-140796600	Flanking Active TSS	HSMM	muscle
43	chr3:140795400-140796800	Flanking Active TSS	NH-A	brain
44	chr3:140795400-140797200	Enhancers	Fetal Intestine Small	intestine
45	chr3:140795400-140797600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr3:140795600-140796400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:140795600-140796400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr3:140795600-140796400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:140795600-140796400	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr3:140795600-140796400	Active TSS	Duodenum Smooth Muscle	Duodenum

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