Variant report

Variant	rs1010858
Chromosome Location	chr2:39102671-39102672
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	GABPA	chr2:39102666-39103497	HL-60	blood:	n/a	n/a
2	POLR2A	chr2:39102607-39103447	U87	brain:	n/a	n/a
3	POLR2A	chr2:39102640-39103411	MCF-7	breast:	n/a	n/a
4	POLR2A	chr2:39102613-39103301	K562	blood:	n/a	n/a
5	POLR2A	chr2:39102523-39103361	K562	blood:	n/a	n/a
6	MXI1	chr2:39102020-39103786	IMR90	lung:	n/a	chr2:39103127-39103142 chr2:39102329-39102338
7	POLR2A	chr2:39102546-39103327	H1-hESC	embryonic stem cell:	n/a	n/a
8	TAF1	chr2:39102581-39103318	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr2:39102641-39103447	U87	brain:	n/a	n/a
10	HCFC1	chr2:39102166-39104264	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr2:39102539-39103303	HepG2	liver:	n/a	n/a
12	HA-E2F1	chr2:39102552-39103633	MCF-7	breast:	n/a	chr2:39103075-39103084
13	SIN3A	chr2:39102421-39103627	H1-hESC	embryonic stem cell:	n/a	chr2:39103155-39103168 chr2:39102713-39102724 chr2:39103152-39103161
14	TAF1	chr2:39102620-39103302	H1-neurons	neurons:	n/a	n/a
15	POLR2A	chr2:39102615-39103328	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr2:39102565-39103268	HL-60	blood:	n/a	n/a
17	NR2C2	chr2:39102596-39103592	Hela-S3	cervix:	n/a	chr2:39103109-39103118 chr2:39103114-39103123
18	POLR2A	chr2:39102635-39103294	NB4	blood:	n/a	n/a
19	GABPA	chr2:39102591-39103496	A549	lung:	n/a	n/a
20	SP1	chr2:39102607-39103441	A549	lung:	n/a	chr2:39103258-39103272
21	TEAD4	chr2:39102639-39103316	K562	blood:	n/a	n/a
22	POLR2A	chr2:39102613-39103237	SK-N-SH	brain:	n/a	n/a
23	CREB1	chr2:39102468-39103440	HepG2	liver:	n/a	n/a
24	UBTF	chr2:39102662-39103364	K562	blood:	n/a	n/a
25	CHD2	chr2:39102623-39103263	K562	blood:	n/a	n/a
26	JUND	chr2:39102534-39103366	A549	lung:	n/a	chr2:39103073-39103082
27	CREB1	chr2:39102526-39103474	K562	blood:	n/a	n/a
28	E2F6	chr2:39102623-39103514	K562	blood:	n/a	chr2:39103075-39103084
29	POLR2A	chr2:39102648-39103240	A549	lung:	n/a	n/a
30	MAX	chr2:39102664-39103380	HepG2	liver:	n/a	n/a
31	POLR2A	chr2:39102548-39103374	Hela-S3	cervix:	n/a	n/a
32	GABPA	chr2:39102565-39103548	SK-N-SH	brain:	n/a	n/a
33	HMGN3	chr2:39102571-39103384	K562	blood:	n/a	n/a
34	TCF7L2	chr2:39102626-39103286	HCT-116	colon:	n/a	n/a
35	TAF1	chr2:39102587-39103249	SK-N-SH	brain:	n/a	n/a
36	REST	chr2:39102199-39103621	H1-neurons	neurons:	n/a	chr2:39103155-39103164 chr2:39102392-39102401 chr2:39103158-39103171
37	MXI1	chr2:39102284-39103345	HepG2	liver:	n/a	chr2:39103127-39103142 chr2:39102329-39102338
38	JUND	chr2:39102550-39103582	GM12878	blood:	n/a	chr2:39103073-39103082
39	RCOR1	chr2:39102659-39103244	K562	blood:	n/a	n/a
40	CHD2	chr2:39102550-39103317	Hela-S3	cervix:	n/a	n/a
41	GABPA	chr2:39102486-39103485	SK-N-SH	brain:	n/a	n/a
42	TAF1	chr2:39102670-39103317	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr2:39102574-39103217	GM12891	blood:	n/a	n/a
44	ELF1	chr2:39102649-39103237	K562	blood:	n/a	chr2:39103106-39103117 chr2:39103106-39103115 chr2:39103107-39103116 chr2:39103106-39103117
45	SIN3AK20	chr2:39102355-39103687	MCF-7	breast:	n/a	n/a
46	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
47	MYBL2	chr2:39102547-39103453	HepG2	liver:	n/a	n/a
48	POLR2A	chr2:39102655-39103298	A549	lung:	n/a	n/a
49	HEY1	chr2:39102627-39103294	HepG2	liver:	n/a	n/a
50	HEY1	chr2:39102610-39103332	K562	blood:	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
ENSG00000163214	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1010859	0.94[EUR][1000 genomes]
rs10204999	0.87[AMR][1000 genomes]
rs11124651	0.89[AFR][1000 genomes]
rs11124654	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11124655	0.81[AMR][1000 genomes]
rs1131752	0.82[EUR][1000 genomes]
rs11675110	0.81[AFR][1000 genomes]
rs11689954	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12373604	0.91[AFR][1000 genomes]
rs12465365	0.84[AFR][1000 genomes]
rs12617734	0.85[AFR][1000 genomes]
rs12621073	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12712627	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12712628	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13029388	0.89[AFR][1000 genomes]
rs13035182	0.81[EUR][1000 genomes]
rs17422748	0.84[EUR][1000 genomes]
rs1901289	0.91[AFR][1000 genomes]
rs2060743	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099940	0.84[EUR][1000 genomes]
rs3099941	0.85[EUR][1000 genomes]
rs3099942	0.88[EUR][1000 genomes]
rs3099958	0.85[EUR][1000 genomes]
rs3099959	0.83[EUR][1000 genomes]
rs3099998	0.84[EUR][1000 genomes]
rs373300	0.90[AMR][1000 genomes]
rs389023	0.84[AMR][1000 genomes]
rs4133043	0.86[AFR][1000 genomes]
rs4641916	0.88[AFR][1000 genomes]
rs4670899	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6544180	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6706091	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6706186	0.86[AMR][1000 genomes]
rs6710418	0.89[AFR][1000 genomes]
rs6732083	0.86[AFR][1000 genomes]
rs6738403	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6741088	0.89[ASN][1000 genomes]
rs6744514	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6754902	0.82[EUR][1000 genomes]
rs7598922	0.91[AFR][1000 genomes]
rs9808136	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1010858	DHX57	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39101800-39103000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:39101800-39103400	Active TSS	Sigmoid Colon	Sigmoid Colon
3	chr2:39101800-39103600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:39101800-39103600	Active TSS	A549	lung
5	chr2:39101800-39104200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr2:39101800-39104200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr2:39102000-39102800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr2:39102000-39102800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:39102000-39102800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr2:39102000-39103200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:39102000-39103400	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr2:39102000-39103400	Active TSS	Fetal Muscle Leg	muscle
13	chr2:39102000-39103600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:39102000-39103600	Active TSS	Brain Angular Gyrus	brain
15	chr2:39102000-39103800	Active TSS	H9 Cell Line	embryonic stem cell
16	chr2:39102000-39103800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:39102000-39103800	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr2:39102000-39103800	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr2:39102000-39103800	Active TSS	Fetal Stomach	stomach
20	chr2:39102000-39104000	Active TSS	H1 Cell Line	embryonic stem cell
21	chr2:39102000-39104000	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr2:39102000-39104000	Active TSS	Muscle Satellite Cultured Cells	--
23	chr2:39102000-39104200	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr2:39102000-39104200	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr2:39102000-39104200	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr2:39102200-39102800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:39102200-39102800	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr2:39102200-39102800	Flanking Active TSS	Liver	Liver
29	chr2:39102200-39102800	Flanking Active TSS	Placenta	Placenta
30	chr2:39102200-39102800	Flanking Active TSS	Thymus	Thymus
31	chr2:39102200-39103200	Active TSS	Primary T cells fromperipheralblood	blood
32	chr2:39102200-39103200	Active TSS	Fetal Muscle Trunk	muscle
33	chr2:39102200-39103400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:39102200-39103400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:39102200-39103400	Active TSS	Fetal Thymus	thymus
36	chr2:39102200-39103400	Active TSS	Psoas Muscle	Psoas
37	chr2:39102200-39103600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:39102200-39103600	Active TSS	Brain Substantia Nigra	brain
39	chr2:39102200-39103600	Active TSS	Fetal Intestine Small	intestine
40	chr2:39102200-39103600	Active TSS	Left Ventricle	heart
41	chr2:39102200-39103800	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr2:39102200-39103800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr2:39102200-39103800	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr2:39102200-39103800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:39102200-39103800	Active TSS	Gastric	stomach
46	chr2:39102200-39103800	Active TSS	Stomach Mucosa	stomach
47	chr2:39102200-39103800	Active TSS	NHDF-Ad	bronchial
48	chr2:39102200-39104000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:39102200-39104000	Active TSS	Ovary	ovary
50	chr2:39102400-39102800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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