Variant report

Variant	rs744039
Chromosome Location	chr15:51973373-51973374
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	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	MXI1	chr15:51973300-51974057	H1-hESC	embryonic stem cell:	n/a	n/a
4	E2F6	chr15:51973357-51973908	A549	lung:	n/a	chr15:51973831-51973843 chr15:51973597-51973608
5	CREB1	chr15:51973354-51974000	H1-hESC	embryonic stem cell:	n/a	n/a
6	REST	chr15:51973297-51974031	PANC-1	pancreas:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
7	REST	chr15:51973366-51973846	U87	brain:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
8	REST	chr15:51973191-51974175	PFSK-1	brain:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
9	REST	chr15:51973372-51974155	H1-hESC	embryonic stem cell:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
10	POLR2A	chr15:51973146-51974321	H1-hESC	embryonic stem cell:	n/a	n/a
11	BHLHE40	chr15:51973338-51974136	K562	blood:	n/a	n/a
12	REST	chr15:51973063-51974211	MCF-7	breast:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
13	GABPA	chr15:51973363-51973994	K562	blood:	n/a	n/a
14	POLR2A	chr15:51973210-51974218	H1-hESC	embryonic stem cell:	n/a	n/a
15	JUN	chr15:51973029-51974111	K562	blood:	n/a	chr15:51973578-51973588
16	REST	chr15:51973226-51974203	HCT-116	colon:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
17	TAF1	chr15:51973326-51973937	H1-neurons	neurons:	n/a	n/a
18	REST	chr15:51973197-51974173	Hela-S3	cervix:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
19	REST	chr15:51973163-51974286	ECC-1	luminal epithelium:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
20	REST	chr15:51973032-51974307	PANC-1	pancreas:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
21	MAX	chr15:51973359-51973983	ECC-1	luminal epithelium:	n/a	chr15:51973599-51973609
22	E2F6	chr15:51973312-51973902	K562	blood:	n/a	chr15:51973831-51973843 chr15:51973597-51973608
23	REST	chr15:51973298-51974061	HCT-116	colon:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
24	REST	chr15:51973336-51974042	HepG2	liver:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
25	REST	chr15:51973286-51974075	GM12878	blood:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
26	REST	chr15:51972970-51974549	HL-60	blood:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
27	MAX	chr15:51973281-51974015	H1-hESC	embryonic stem cell:	n/a	chr15:51973599-51973609
28	MAX	chr15:51973281-51974132	H1-hESC	embryonic stem cell:	n/a	chr15:51973599-51973609
29	TAF1	chr15:51973239-51974203	H1-neurons	neurons:	n/a	n/a
30	NRF1	chr15:51973330-51973956	SK-N-SH	brain:	n/a	n/a
31	MXI1	chr15:51972837-51974576	SK-N-SH	brain:	n/a	n/a
32	E2F6	chr15:51973155-51974040	H1-hESC	embryonic stem cell:	n/a	chr15:51973831-51973843 chr15:51973597-51973608
33	RFX5	chr15:51973361-51973382	K562	blood:	n/a	n/a
34	REST	chr15:51973141-51974258	ECC-1	luminal epithelium:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
35	HCFC1	chr15:51973177-51974082	K562	blood:	n/a	n/a
36	CREB1	chr15:51973330-51973965	K562	blood:	n/a	n/a
37	YY1	chr15:51973369-51973891	H1-hESC	embryonic stem cell:	n/a	n/a
38	CREB1	chr15:51973356-51974058	K562	blood:	n/a	n/a
39	TAF1	chr15:51973249-51974143	H1-hESC	embryonic stem cell:	n/a	n/a
40	REST	chr15:51972940-51974158	A549	lung:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
41	POLR2A	chr15:51972968-51974285	H1-neurons	neurons:	n/a	n/a
42	REST	chr15:51972752-51974643	H1-neurons	neurons:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
43	CBX3	chr15:51973259-51973943	K562	blood:	n/a	chr15:51973517-51973528
44	REST	chr15:51973329-51974109	Hela-S3	cervix:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
45	REST	chr15:51973314-51974212	HL-60	blood:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
46	SIN3A	chr15:51973288-51974310	H1-hESC	embryonic stem cell:	n/a	chr15:51973903-51973912
47	REST	chr15:51973322-51974031	SK-N-SH	brain:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
48	REST	chr15:51973295-51974158	HepG2	liver:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
49	REST	chr15:51973267-51974189	PFSK-1	brain:	n/a	chr15:51973725-51973734 chr15:51973727-51973734
50	TBP	chr15:51973321-51974279	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
SCG3	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10519313	0.91[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs10851502	0.87[YRI][hapmap]
rs11070857	0.89[GIH][hapmap]
rs11070859	0.81[YRI][hapmap]
rs11070863	0.91[ASN][1000 genomes]
rs11631725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634180	0.82[YRI][hapmap]
rs11634955	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11635216	0.91[GIH][hapmap];0.81[TSI][hapmap]
rs11637716	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11638106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638154	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12372948	0.89[GIH][hapmap];0.81[TSI][hapmap]
rs12440990	0.88[YRI][hapmap]
rs1456299	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1456300	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2054166	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2124592	0.81[YRI][hapmap]
rs2124875	0.88[YRI][hapmap]
rs2168474	0.89[ASN][1000 genomes]
rs2278989	0.91[GIH][hapmap];0.80[MEX][hapmap]
rs2278990	0.91[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs2305716	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2414105	0.91[GIH][hapmap];0.81[TSI][hapmap]
rs2414106	0.91[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs2414109	0.91[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs2414111	0.93[GIH][hapmap]
rs2607119	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2622775	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2652594	0.94[JPT][hapmap]
rs28576876	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4774597	0.84[YRI][hapmap]
rs4775953	0.91[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs4775955	0.87[GIH][hapmap];0.81[TSI][hapmap]
rs4775960	0.89[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs4775961	0.89[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs4775968	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55982453	0.93[ASN][1000 genomes]
rs60060794	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6493505	0.81[YRI][hapmap]
rs7167760	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap]
rs7168749	0.89[ASN][1000 genomes]
rs7170217	0.85[YRI][hapmap]
rs7170444	0.83[YRI][hapmap]
rs7170980	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs7171884	0.94[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs7174495	0.88[YRI][hapmap]
rs7177720	0.89[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs7183479	0.94[CHB][hapmap];0.96[YRI][hapmap]
rs8023455	0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs8033234	0.94[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs8034197	0.91[ASN][1000 genomes]
rs8037167	0.91[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs8037340	0.91[ASN][1000 genomes]
rs8042221	0.91[GIH][hapmap];0.81[TSI][hapmap]
rs8042840	0.91[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs9944241	0.91[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]

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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs744039	TMOD2	cis	cerebellum	SCAN
rs744039	BCL2L10	cis	parietal	SCAN
rs744039	TMOD2	cis	parietal	SCAN
rs744039	DMXL2	cis	lymphoblastoid	seeQTL
rs744039	ARPP19	cis	parietal	SCAN
rs744039	SCG3	cis	cerebellum	SCAN
rs744039	DMXL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51966600-51973400	Weak transcription	Right Atrium	heart
2	chr15:51968800-51973400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:51972800-51973600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr15:51972800-51973600	Flanking Active TSS	Brain Hippocampus Middle	brain
5	chr15:51973000-51973400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:51973000-51973400	Flanking Active TSS	Brain Anterior Caudate	brain
7	chr15:51973000-51973400	Flanking Active TSS	Brain Cingulate Gyrus	brain
8	chr15:51973000-51973600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:51973000-51973600	Flanking Active TSS	Brain Angular Gyrus	brain
10	chr15:51973000-51974200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:51973000-51974400	Active TSS	H9 Cell Line	embryonic stem cell
12	chr15:51973000-51974400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:51973000-51974600	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr15:51973000-51974600	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr15:51973000-51974800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr15:51973000-51975000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:51973000-51975000	Active TSS	Fetal Brain Female	brain
18	chr15:51973000-51975400	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr15:51973200-51973400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr15:51973200-51973400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr15:51973200-51973400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
22	chr15:51973200-51973400	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:51973200-51973400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:51973200-51973400	Enhancers	Adipose Nuclei	Adipose
25	chr15:51973200-51973400	Active TSS	Brain Substantia Nigra	brain
26	chr15:51973200-51973400	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr15:51973200-51973400	Active TSS	Fetal Brain Male	brain
28	chr15:51973200-51973400	Bivalent/Poised TSS	A549	lung
29	chr15:51973200-51973600	Active TSS	Brain Germinal Matrix	brain
30	chr15:51973200-51973600	Flanking Active TSS	K562	blood
31	chr15:51973200-51974000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:51973200-51974200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:51973200-51974200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
34	chr15:51973200-51974200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr15:51973200-51974200	Enhancers	Placenta	Placenta
36	chr15:51973200-51974400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:51973200-51974600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr15:51973200-51974600	Active TSS	H1 Cell Line	embryonic stem cell
39	chr15:51973200-51974600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr15:51973200-51974800	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr15:51973200-51974800	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr15:51973200-51974800	Active TSS	iPS-15b Cell Line	embryonic stem cell

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