Variant report

Variant	rs897581
Chromosome Location	chr15:51973438-51973439
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	REST	chr15:51973204-51974148	K562	blood:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
2	MAX	chr15:51973194-51973863	H1-hESC	embryonic stem cell:	n/a	chr15:51973599-51973609
3	MAX	chr15:51973377-51973943	A549	lung:	n/a	chr15:51973599-51973609
4	TAF1	chr15:51973427-51973973	PFSK-1	brain:	n/a	n/a
5	MXI1	chr15:51973300-51974057	H1-hESC	embryonic stem cell:	n/a	n/a
6	E2F6	chr15:51973357-51973908	A549	lung:	n/a	chr15:51973831-51973843 chr15:51973597-51973608
7	ZNF263	chr15:51973433-51974122	HEK293-T-REx	kidney:	n/a	chr15:51973628-51973649
8	CREB1	chr15:51973354-51974000	H1-hESC	embryonic stem cell:	n/a	n/a
9	REST	chr15:51973297-51974031	PANC-1	pancreas:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
10	POLR2A	chr15:51973422-51973801	H1-hESC	embryonic stem cell:	n/a	n/a
11	REST	chr15:51973366-51973846	U87	brain:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
12	REST	chr15:51973418-51974039	H1-neurons	neurons:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
13	POLR2A	chr15:51973380-51974116	H1-hESC	embryonic stem cell:	n/a	n/a
14	ATF3	chr15:51973405-51973799	K562	blood:	n/a	chr15:51973587-51973607 chr15:51973759-51973768
15	REST	chr15:51973191-51974175	PFSK-1	brain:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
16	REST	chr15:51973430-51974094	K562	blood:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
17	REST	chr15:51973372-51974155	H1-hESC	embryonic stem cell:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
18	POLR2A	chr15:51973146-51974321	H1-hESC	embryonic stem cell:	n/a	n/a
19	BHLHE40	chr15:51973338-51974136	K562	blood:	n/a	n/a
20	REST	chr15:51973063-51974211	MCF-7	breast:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
21	ZMIZ1	chr15:51973383-51973886	K562	blood:	n/a	n/a
22	MYC	chr15:51973398-51973984	K562	blood:	n/a	chr15:51973599-51973609
23	TAF1	chr15:51973417-51974104	H1-hESC	embryonic stem cell:	n/a	n/a
24	GABPA	chr15:51973363-51973994	K562	blood:	n/a	n/a
25	POLR2A	chr15:51973210-51974218	H1-hESC	embryonic stem cell:	n/a	n/a
26	JUN	chr15:51973029-51974111	K562	blood:	n/a	chr15:51973578-51973588
27	POLR2A	chr15:51973423-51973778	K562	blood:	n/a	n/a
28	REST	chr15:51973226-51974203	HCT-116	colon:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
29	REST	chr15:51973374-51974083	H1-hESC	embryonic stem cell:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
30	TAF1	chr15:51973326-51973937	H1-neurons	neurons:	n/a	n/a
31	YY1	chr15:51973420-51973794	K562	blood:	n/a	n/a
32	REST	chr15:51973197-51974173	Hela-S3	cervix:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
33	REST	chr15:51973163-51974286	ECC-1	luminal epithelium:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
34	POLR2A	chr15:51973388-51974030	K562	blood:	n/a	n/a
35	YY1	chr15:51973398-51973789	SK-N-SH_RA	brain:	n/a	n/a
36	CREB1	chr15:51973435-51973945	GM12878	blood:	n/a	n/a
37	HEY1	chr15:51973395-51973742	K562	blood:	n/a	chr15:51973528-51973543
38	REST	chr15:51973032-51974307	PANC-1	pancreas:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
39	MAX	chr15:51973359-51973983	ECC-1	luminal epithelium:	n/a	chr15:51973599-51973609
40	E2F6	chr15:51973312-51973902	K562	blood:	n/a	chr15:51973831-51973843 chr15:51973597-51973608
41	FOXP2	chr15:51973428-51973881	PFSK-1	brain:	n/a	n/a
42	REST	chr15:51973298-51974061	HCT-116	colon:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
43	REST	chr15:51973336-51974042	HepG2	liver:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
44	REST	chr15:51973424-51973870	GM12878	blood:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
45	REST	chr15:51973286-51974075	GM12878	blood:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
46	REST	chr15:51972970-51974549	HL-60	blood:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
47	MAX	chr15:51973281-51974015	H1-hESC	embryonic stem cell:	n/a	chr15:51973599-51973609
48	POLR2A	chr15:51973408-51973797	K562	blood:	n/a	n/a
49	CTBP2	chr15:51973379-51974028	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAX	chr15:51973281-51974132	H1-hESC	embryonic stem cell:	n/a	chr15:51973599-51973609

Variant related genes	Relation type
SCG3	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1017679	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10851501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11070861	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11857716	0.80[AMR][1000 genomes]
rs12324531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12441057	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12708427	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12901452	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12904173	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12904583	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1378892	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378893	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378894	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1378895	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1456295	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1456297	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471072	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1531157	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551657	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17524750	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17524906	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1840707	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1902595	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1902596	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2252220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2414112	1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2606134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606137	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606138	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606139	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606141	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2606143	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2606145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2606146	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2607110	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2607112	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2607116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607117	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2622768	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2622769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622770	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28408214	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34448759	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34532503	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34662965	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34929849	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35011964	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4465557	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4774594	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4775954	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55725532	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60694229	0.83[AMR][1000 genomes]
rs6493507	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6493511	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493512	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs716986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7180329	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7181921	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8025974	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8027162	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8029731	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs956171	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9672605	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9944266	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv904219	chr15:51851999-51977159	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
3	nsv457139	chr15:51854718-51977159	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
4	nsv569407	chr15:51854718-51977159	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
5	nsv1035967	chr15:51949866-52008736	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51972800-51973600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr15:51972800-51973600	Flanking Active TSS	Brain Hippocampus Middle	brain
3	chr15:51973000-51973600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:51973000-51973600	Flanking Active TSS	Brain Angular Gyrus	brain
5	chr15:51973000-51974200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:51973000-51974400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr15:51973000-51974400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:51973000-51974600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr15:51973000-51974600	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr15:51973000-51974800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr15:51973000-51975000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:51973000-51975000	Active TSS	Fetal Brain Female	brain
13	chr15:51973000-51975400	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr15:51973200-51973600	Active TSS	Brain Germinal Matrix	brain
15	chr15:51973200-51973600	Flanking Active TSS	K562	blood
16	chr15:51973200-51974000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:51973200-51974200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:51973200-51974200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
19	chr15:51973200-51974200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr15:51973200-51974200	Enhancers	Placenta	Placenta
21	chr15:51973200-51974400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr15:51973200-51974600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr15:51973200-51974600	Active TSS	H1 Cell Line	embryonic stem cell
24	chr15:51973200-51974600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:51973200-51974800	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr15:51973200-51974800	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr15:51973200-51974800	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr15:51973400-51973600	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr15:51973400-51973600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:51973400-51973600	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:51973400-51973600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
32	chr15:51973400-51973600	Bivalent Enhancer	Primary T cells from cord blood	blood
33	chr15:51973400-51973600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
34	chr15:51973400-51973600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:51973400-51973600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:51973400-51973600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:51973400-51973600	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr15:51973400-51973600	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr15:51973400-51973600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
40	chr15:51973400-51973600	Flanking Active TSS	Fetal Brain Male	brain
41	chr15:51973400-51973600	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
42	chr15:51973400-51973600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
43	chr15:51973400-51973600	Enhancers	Fetal Muscle Leg	muscle
44	chr15:51973400-51973600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
45	chr15:51973400-51973600	Bivalent Enhancer	Thymus	Thymus
46	chr15:51973400-51973600	Bivalent Enhancer	HMEC	breast
47	chr15:51973400-51973600	Bivalent Enhancer	HUVEC	blood vessel
48	chr15:51973400-51973600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
49	chr15:51973400-51973600	Flanking Active TSS	NH-A	brain
50	chr15:51973400-51973800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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