Variant report

Variant	rs2606134
Chromosome Location	chr15:51973650-51973651
allele	C/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	REST	chr15:51973204-51974148	K562	blood:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
2	CTCF	chr15:51973560-51973710	BE2_C	brain:	n/a	chr15:51973599-51973612 chr15:51973648-51973661
3	JUND	chr15:51973494-51973906	K562	blood:	n/a	chr15:51973578-51973588
4	MAX	chr15:51973194-51973863	H1-hESC	embryonic stem cell:	n/a	chr15:51973599-51973609
5	MAX	chr15:51973377-51973943	A549	lung:	n/a	chr15:51973599-51973609
6	TAF1	chr15:51973427-51973973	PFSK-1	brain:	n/a	n/a
7	MXI1	chr15:51973300-51974057	H1-hESC	embryonic stem cell:	n/a	n/a
8	E2F6	chr15:51973357-51973908	A549	lung:	n/a	chr15:51973831-51973843 chr15:51973597-51973608
9	ZNF263	chr15:51973433-51974122	HEK293-T-REx	kidney:	n/a	chr15:51973628-51973649
10	SIN3AK20	chr15:51973514-51973978	PFSK-1	brain:	n/a	n/a
11	SP4	chr15:51973460-51973917	H1-hESC	embryonic stem cell:	n/a	n/a
12	RCOR1	chr15:51973444-51974226	K562	blood:	n/a	n/a
13	CREB1	chr15:51973354-51974000	H1-hESC	embryonic stem cell:	n/a	n/a
14	E2F6	chr15:51973518-51973797	K562	blood:	n/a	chr15:51973597-51973608
15	SIN3AK20	chr15:51973532-51973914	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr15:51973521-51973908	SK-N-SH	brain:	n/a	chr15:51973599-51973609
17	REST	chr15:51973297-51974031	PANC-1	pancreas:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
18	POLR2A	chr15:51973422-51973801	H1-hESC	embryonic stem cell:	n/a	n/a
19	REST	chr15:51973366-51973846	U87	brain:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
20	REST	chr15:51973418-51974039	H1-neurons	neurons:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
21	MAFK	chr15:51973524-51973856	K562	blood:	n/a	n/a
22	NRF1	chr15:51973459-51973822	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr15:51973380-51974116	H1-hESC	embryonic stem cell:	n/a	n/a
24	ATF3	chr15:51973405-51973799	K562	blood:	n/a	chr15:51973587-51973607 chr15:51973759-51973768
25	REST	chr15:51973191-51974175	PFSK-1	brain:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
26	REST	chr15:51973430-51974094	K562	blood:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
27	REST	chr15:51973372-51974155	H1-hESC	embryonic stem cell:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
28	POLR2A	chr15:51973146-51974321	H1-hESC	embryonic stem cell:	n/a	n/a
29	SIN3AK20	chr15:51973496-51973829	SK-N-SH	brain:	n/a	n/a
30	BHLHE40	chr15:51973338-51974136	K562	blood:	n/a	n/a
31	CCNT2	chr15:51973439-51973965	K562	blood:	n/a	chr15:51973766-51973775
32	REST	chr15:51973063-51974211	MCF-7	breast:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
33	CBX3	chr15:51973504-51973836	K562	blood:	n/a	chr15:51973517-51973528
34	ZMIZ1	chr15:51973383-51973886	K562	blood:	n/a	n/a
35	UBTF	chr15:51973508-51973943	K562	blood:	n/a	n/a
36	TEAD4	chr15:51973518-51973831	H1-hESC	embryonic stem cell:	n/a	n/a
37	REST	chr15:51973546-51973859	GM12878	blood:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
38	ZNF143	chr15:51973542-51973893	GM12878	blood:	n/a	chr15:51973706-51973724
39	MYC	chr15:51973398-51973984	K562	blood:	n/a	chr15:51973599-51973609
40	IRF1	chr15:51973521-51973900	K562	blood:	n/a	chr15:51973638-51973647
41	POLR2A	chr15:51973598-51973680	MCF-7	breast:	n/a	n/a
42	TAF1	chr15:51973417-51974104	H1-hESC	embryonic stem cell:	n/a	n/a
43	SMARCB1	chr15:51973527-51974007	K562	blood:	n/a	n/a
44	GABPA	chr15:51973363-51973994	K562	blood:	n/a	n/a
45	POLR2A	chr15:51973210-51974218	H1-hESC	embryonic stem cell:	n/a	n/a
46	JUN	chr15:51973029-51974111	K562	blood:	n/a	chr15:51973578-51973588
47	TEAD4	chr15:51973484-51973930	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr15:51973423-51973778	K562	blood:	n/a	n/a
49	REST	chr15:51973226-51974203	HCT-116	colon:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
50	REST	chr15:51973374-51974083	H1-hESC	embryonic stem cell:	n/a	chr15:51973725-51973734 chr15:51973727-51973734

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];0.82[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];0.89[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];0.85[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];0.89[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];0.89[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];0.89[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];0.88[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];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2414112	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2606136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[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];0.89[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];0.89[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];0.88[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];0.89[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];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];0.89[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];0.89[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];0.89[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];0.89[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]
rs897581	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]
rs956171	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[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:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51973000-51974200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:51973000-51974400	Active TSS	H9 Cell Line	embryonic stem cell
3	chr15:51973000-51974400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:51973000-51974600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr15:51973000-51974600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr15:51973000-51974800	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr15:51973000-51975000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:51973000-51975000	Active TSS	Fetal Brain Female	brain
9	chr15:51973000-51975400	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr15:51973200-51974000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:51973200-51974200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:51973200-51974200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
13	chr15:51973200-51974200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr15:51973200-51974200	Enhancers	Placenta	Placenta
15	chr15:51973200-51974400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:51973200-51974600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr15:51973200-51974600	Active TSS	H1 Cell Line	embryonic stem cell
18	chr15:51973200-51974600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:51973200-51974800	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr15:51973200-51974800	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr15:51973200-51974800	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr15:51973400-51973800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:51973400-51973800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:51973400-51973800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:51973400-51973800	Enhancers	Gastric	stomach
26	chr15:51973400-51973800	Enhancers	Lung	lung
27	chr15:51973400-51973800	Genic enhancers	Right Atrium	heart
28	chr15:51973400-51973800	Enhancers	Right Ventricle	heart
29	chr15:51973400-51973800	Flanking Bivalent TSS/Enh	A549	lung
30	chr15:51973400-51973800	Flanking Bivalent TSS/Enh	NHEK	skin
31	chr15:51973400-51974000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr15:51973400-51974000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
33	chr15:51973400-51974000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
34	chr15:51973400-51974000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:51973400-51974000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:51973400-51974000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:51973400-51974000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
38	chr15:51973400-51974000	Bivalent Enhancer	Left Ventricle	heart
39	chr15:51973400-51974000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
40	chr15:51973400-51974000	Active TSS	Rectal Smooth Muscle	rectum
41	chr15:51973400-51974200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr15:51973400-51974200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:51973400-51974200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:51973400-51974200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr15:51973400-51974200	Enhancers	Liver	Liver
46	chr15:51973400-51974200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr15:51973400-51974200	Enhancers	Pancreas	Pancrea
48	chr15:51973400-51974200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
49	chr15:51973400-51974200	Bivalent Enhancer	Stomach Mucosa	stomach
50	chr15:51973400-51974200	Enhancers	Spleen	Spleen

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