Variant report

Variant	rs1010859
Chromosome Location	chr2:39102528-39102529
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	POLR2A	chr2:39102523-39103361	K562	blood:	n/a	n/a
2	MXI1	chr2:39102020-39103786	IMR90	lung:	n/a	chr2:39103127-39103142 chr2:39102329-39102338
3	HCFC1	chr2:39102166-39104264	Hela-S3	cervix:	n/a	n/a
4	SIN3A	chr2:39102421-39103627	H1-hESC	embryonic stem cell:	n/a	chr2:39103155-39103168 chr2:39102713-39102724 chr2:39103152-39103161
5	CREB1	chr2:39102468-39103440	HepG2	liver:	n/a	n/a
6	CREB1	chr2:39102526-39103474	K562	blood:	n/a	n/a
7	REST	chr2:39102199-39103621	H1-neurons	neurons:	n/a	chr2:39103155-39103164 chr2:39102392-39102401 chr2:39103158-39103171
8	MXI1	chr2:39102284-39103345	HepG2	liver:	n/a	chr2:39103127-39103142 chr2:39102329-39102338
9	GABPA	chr2:39102486-39103485	SK-N-SH	brain:	n/a	n/a
10	SIN3AK20	chr2:39102355-39103687	MCF-7	breast:	n/a	n/a
11	MYC	chr2:39102226-39103351	K562	blood:	n/a	chr2:39102329-39102338 chr2:39102327-39102338 chr2:39102326-39102339 chr2:39102328-39102338 chr2:39102328-39102338 chr2:39102327-39102337
12	POLR2A	chr2:39102431-39103416	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr2:39102304-39103555	MCF10A-Er-Src	breast:	n/a	n/a
14	SMARCB1	chr2:39102496-39103410	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr2:39102523-39103326	GM12878	blood:	n/a	n/a
16	GABPA	chr2:39102492-39103508	K562	blood:	n/a	n/a
17	CREB1	chr2:39102519-39103409	H1-hESC	embryonic stem cell:	n/a	n/a
18	TAF1	chr2:39102333-39103299	H1-neurons	neurons:	n/a	n/a
19	POLR2A	chr2:39102402-39103370	IMR90	lung:	n/a	n/a
20	MAX	chr2:39102463-39103286	NB4	blood:	n/a	n/a
21	SMC3	chr2:39102288-39103425	Hela-S3	cervix:	n/a	chr2:39102839-39102849 chr2:39102753-39102761
22	POLR2A	chr2:39102516-39103273	ProgFib	skin:	n/a	n/a
23	GABPA	chr2:39102255-39103641	A549	lung:	n/a	n/a
24	TAF1	chr2:39102441-39103426	H1-hESC	embryonic stem cell:	n/a	n/a
25	WRNIP1	chr2:39102431-39103380	GM12878	blood:	n/a	n/a
26	TCF12	chr2:39102297-39103408	A549	lung:	n/a	chr2:39102753-39102763
27	MAX	chr2:39102452-39103531	A549	lung:	n/a	n/a
28	MAX	chr2:39102523-39103497	ECC-1	luminal epithelium:	n/a	n/a
29	MYBL2	chr2:39102410-39103789	HepG2	liver:	n/a	n/a
30	POLR2A	chr2:39102358-39103526	HepG2	liver:	n/a	n/a
31	POLR2A	chr2:39102467-39103420	Hela-S3	cervix:	n/a	n/a
32	GTF2F1	chr2:39102409-39103432	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr2:39102517-39103374	SK-N-MC	brain:	n/a	n/a
34	JUND	chr2:39102239-39104280	SK-N-SH	brain:	n/a	chr2:39103073-39103082
35	GABPA	chr2:39102377-39103684	MCF-7	breast:	n/a	n/a
36	CEBPD	chr2:39102512-39103258	HepG2	liver:	n/a	n/a
37	TBP	chr2:39102306-39103425	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr2:39102494-39103353	GM12892	blood:	n/a	n/a
39	GATA2	chr2:39102207-39103383	SH-SY5Y	brain:	n/a	chr2:39102343-39102356
40	MAX	chr2:39102500-39103448	GM12878	blood:	n/a	n/a
41	TBP	chr2:39102401-39103237	HepG2	liver:	n/a	n/a
42	MAX	chr2:39102239-39103795	Hela-S3	cervix:	n/a	chr2:39102329-39102338 chr2:39102327-39102338 chr2:39102326-39102339 chr2:39102328-39102338 chr2:39102328-39102338 chr2:39102327-39102337
43	CBX3	chr2:39102473-39103408	K562	blood:	n/a	n/a
44	MAX	chr2:39102484-39103500	K562	blood:	n/a	n/a
45	MXI1	chr2:39101863-39104341	SK-N-SH	brain:	n/a	chr2:39103127-39103142 chr2:39102329-39102338
46	KAT2A	chr2:39102499-39102723	Hela-S3	cervix:	n/a	n/a
47	NR2C2	chr2:39102444-39103719	GM12878	blood:	n/a	chr2:39103109-39103118 chr2:39103114-39103123
48	MAZ	chr2:39102519-39103310	GM12878	blood:	n/a	n/a
49	SREBP1	chr2:39101910-39104141	GM12878	blood:	n/a	chr2:39103128-39103142 chr2:39103701-39103711
50	POLR2A	chr2:39102252-39103487	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:38976877..38979785-chr2:39100480..39105632,13	K562	blood:
2	chr2:38973415..38975366-chr2:39100938..39103537,2	K562	blood:
3	chr2:39092323..39097069-chr2:39100019..39103136,5	MCF-7	breast:
4	chr2:38976936..38979845-chr2:39101241..39105632,7	K562	blood:

Variant related genes	Relation type
MORN2	TF binding region
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000163214	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1010858	0.94[EUR][1000 genomes]
rs10181808	0.86[AMR][1000 genomes]
rs10865143	0.88[JPT][hapmap]
rs11124654	0.86[EUR][1000 genomes]
rs1131752	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11681583	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11689954	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs11898812	0.88[JPT][hapmap]
rs12621073	0.83[EUR][1000 genomes]
rs12712625	0.81[GIH][hapmap]
rs12712626	0.81[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap]
rs12712627	0.81[GIH][hapmap]
rs12712628	0.91[EUR][1000 genomes]
rs13035182	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17422748	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1901289	0.81[GIH][hapmap]
rs1979143	0.83[ASW][hapmap];0.88[JPT][hapmap]
rs2373469	0.86[AFR][1000 genomes]
rs2373471	0.86[AFR][1000 genomes]
rs3099940	0.85[EUR][1000 genomes]
rs3099941	0.80[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs3099942	0.85[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3099945	0.82[GIH][hapmap];0.84[MEX][hapmap]
rs3099946	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3099955	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3099956	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs3099958	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3099959	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3099968	0.83[ASW][hapmap];0.88[JPT][hapmap]
rs3099990	0.88[JPT][hapmap]
rs3099995	0.84[AFR][1000 genomes]
rs3099998	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3100000	0.88[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3112159	1.00[ASW][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap]
rs3112163	1.00[ASW][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.96[LWK][hapmap];0.84[MKK][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3112166	0.93[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3112175	0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3112184	0.88[JPT][hapmap]
rs3112188	0.88[JPT][hapmap]
rs3112189	0.88[JPT][hapmap]
rs3112191	1.00[JPT][hapmap]
rs3112192	0.88[JPT][hapmap]
rs3112196	0.88[JPT][hapmap]
rs3112215	0.80[CEU][hapmap]
rs3134637	0.88[JPT][hapmap]
rs373300	0.81[MEX][hapmap];0.84[TSI][hapmap]
rs384007	0.81[AMR][1000 genomes]
rs384421	0.81[AMR][1000 genomes]
rs3923144	0.90[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap]
rs434696	0.81[AMR][1000 genomes]
rs4670266	0.81[CHB][hapmap]
rs4670268	0.84[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4670899	0.84[CEU][hapmap];0.89[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs4670900	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61736780	0.82[AFR][1000 genomes]
rs6544180	0.81[EUR][1000 genomes]
rs6706091	0.84[EUR][1000 genomes]
rs6717670	0.88[JPT][hapmap]
rs6736353	0.86[AFR][1000 genomes]
rs6738069	0.84[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6744514	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs6754902	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72797376	0.83[AFR][1000 genomes]
rs72797386	0.85[AFR][1000 genomes]
rs72797392	0.86[AFR][1000 genomes]
rs72797402	0.81[AFR][1000 genomes]
rs7565111	1.00[CHB][hapmap]
rs7598922	0.81[GIH][hapmap]
rs8179664	0.90[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs9808136	0.84[CEU][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv2692	chr2:39065768-39111871	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1010859	DHX57	cis	cerebellum	SCAN
rs1010859	ITGB1	trans	parietal	SCAN
rs1010859	MORN2	cis	parietal	SCAN
rs1010859	DHX57	Cis_1M	lymphoblastoid	RTeQTL
rs1010859	MFN1	trans	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39101800-39102600	Flanking Active TSS	Dnd41	blood
2	chr2:39101800-39103000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:39101800-39103400	Active TSS	Sigmoid Colon	Sigmoid Colon
4	chr2:39101800-39103600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:39101800-39103600	Active TSS	A549	lung
6	chr2:39101800-39104200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr2:39101800-39104200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr2:39102000-39102600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:39102000-39102600	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr2:39102000-39102600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr2:39102000-39102600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:39102000-39102600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:39102000-39102600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:39102000-39102600	Flanking Active TSS	Brain Anterior Caudate	brain
15	chr2:39102000-39102600	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr2:39102000-39102600	Flanking Active TSS	Fetal Brain Male	brain
17	chr2:39102000-39102600	Flanking Active TSS	Fetal Heart	heart
18	chr2:39102000-39102600	Flanking Active TSS	Fetal Kidney	kidney
19	chr2:39102000-39102600	Flanking Active TSS	HSMMtube	muscle
20	chr2:39102000-39102600	Flanking Active TSS	HUVEC	blood vessel
21	chr2:39102000-39102600	Flanking Active TSS	NH-A	brain
22	chr2:39102000-39102600	Flanking Active TSS	NHLF	lung
23	chr2:39102000-39102800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr2:39102000-39102800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:39102000-39102800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr2:39102000-39103200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:39102000-39103400	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr2:39102000-39103400	Active TSS	Fetal Muscle Leg	muscle
29	chr2:39102000-39103600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:39102000-39103600	Active TSS	Brain Angular Gyrus	brain
31	chr2:39102000-39103800	Active TSS	H9 Cell Line	embryonic stem cell
32	chr2:39102000-39103800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:39102000-39103800	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr2:39102000-39103800	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr2:39102000-39103800	Active TSS	Fetal Stomach	stomach
36	chr2:39102000-39104000	Active TSS	H1 Cell Line	embryonic stem cell
37	chr2:39102000-39104000	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr2:39102000-39104000	Active TSS	Muscle Satellite Cultured Cells	--
39	chr2:39102000-39104200	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr2:39102000-39104200	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr2:39102000-39104200	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr2:39102200-39102600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr2:39102200-39102600	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr2:39102200-39102600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:39102200-39102600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr2:39102200-39102600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr2:39102200-39102600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr2:39102200-39102600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr2:39102200-39102600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr2:39102200-39102600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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