Variant report

Variant	rs7075288
Chromosome Location	chr10:44070587-44070588
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	MXI1	chr10:44068477-44070901	SK-N-SH	brain:	n/a	n/a
2	MAZ	chr10:44069205-44070656	IMR90	lung:	n/a	n/a
3	E2F6	chr10:44070306-44070600	K562	blood:	n/a	n/a
4	SETDB1	chr10:44069820-44071203	U2OS	brain:	n/a	chr10:44070058-44070082
5	CEBPB	chr10:44069447-44070611	Hela-S3	cervix:	n/a	chr10:44070313-44070326
6	MAFK	chr10:44069844-44070734	K562	blood:	n/a	chr10:44070165-44070174
7	SETDB1	chr10:44069248-44070615	K562	blood:	n/a	chr10:44070058-44070082
8	CBX3	chr10:44069117-44070826	K562	blood:	n/a	n/a
9	MYC	chr10:44068894-44070710	K562	blood:	n/a	n/a
10	TBL1XR1	chr10:44069825-44070716	K562	blood:	n/a	n/a
11	POLR2A	chr10:44068596-44070593	Hela-S3	cervix:	n/a	n/a
12	HCFC1	chr10:44069138-44070810	Hela-S3	cervix:	n/a	n/a
13	E2F6	chr10:44070398-44070648	K562	blood:	n/a	n/a
14	POLR2A	chr10:44070541-44070589	MCF-7	breast:	n/a	n/a
15	E2F6	chr10:44068809-44070750	K562	blood:	n/a	chr10:44069361-44069371 chr10:44069731-44069740 chr10:44069844-44069853 chr10:44068925-44068934 chr10:44069814-44069824
16	MYC	chr10:44068980-44070593	K562	blood:	n/a	n/a
17	GTF2F1	chr10:44069832-44070699	Hela-S3	cervix:	n/a	n/a
18	SIN3A	chr10:44070577-44070587	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr10:44070313-44070687	K562	blood:	n/a	n/a
20	POLR2A	chr10:44069474-44070589	K562	blood:	n/a	n/a
21	BHLHE40	chr10:44068892-44070821	K562	blood:	n/a	chr10:44069738-44069754 chr10:44069201-44069217 chr10:44069834-44069850 chr10:44069950-44069966
22	MXI1	chr10:44069241-44070660	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:44063474..44065679-chr10:44068799..44071087,3	MCF-7	breast:
2	chr10:44068620..44071892-chr10:44099602..44104778,6	MCF-7	breast:

Variant related genes	Relation type
ZNF239	TF binding region
ENSG00000198298	Chromatin interaction
ENSG00000232004	Chromatin interaction
ENSG00000196793	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11238575	1.00[CHB][hapmap]
rs11238595	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs1338567	1.00[ASN][1000 genomes]
rs1338568	1.00[ASN][1000 genomes]
rs1338569	1.00[ASN][1000 genomes]
rs1361227	1.00[ASN][1000 genomes]
rs1361228	1.00[ASN][1000 genomes]
rs17153601	1.00[CHB][hapmap]
rs17154024	0.90[CEU][hapmap]
rs1832466	1.00[ASN][1000 genomes]
rs1832472	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2261637	1.00[CHB][hapmap]
rs2265955	1.00[CHB][hapmap]
rs2393949	1.00[CHB][hapmap]
rs2819025	1.00[CHB][hapmap]
rs2999237	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2999238	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2999239	1.00[ASN][1000 genomes]
rs2999240	1.00[ASN][1000 genomes]
rs2999241	1.00[ASN][1000 genomes]
rs2999242	1.00[ASN][1000 genomes]
rs2999290	1.00[CHB][hapmap]
rs3006364	1.00[ASN][1000 genomes]
rs3006365	1.00[ASN][1000 genomes]
rs3006378	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006381	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006382	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006389	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4948727	1.00[CHB][hapmap]
rs7068859	1.00[CHB][hapmap]
rs7069748	1.00[CHB][hapmap]
rs7079327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7084457	1.00[ASN][1000 genomes]
rs7084621	1.00[CHB][hapmap]
rs72787457	1.00[ASN][1000 genomes]
rs72787487	1.00[ASN][1000 genomes]
rs7478426	1.00[CHB][hapmap]
rs7908842	1.00[ASN][1000 genomes]
rs7922477	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1798523	chr10:44051698-44070754	Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7075288	ZNF239	cis	multi-tissue	Pritchard
rs7075288	ZNF239	cis	Liver	GTEx
rs7075288	ZNF239	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44068200-44070600	Active TSS	Fetal Kidney	kidney
2	chr10:44068800-44070600	Active TSS	NHLF	lung
3	chr10:44069000-44070600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr10:44069000-44070600	Active TSS	HSMM	muscle
5	chr10:44069000-44070800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr10:44069000-44070800	ZNF genes & repeats	GM12878-XiMat	blood
7	chr10:44069200-44070600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr10:44069200-44070600	Active TSS	Aorta	Aorta
9	chr10:44069200-44070600	Active TSS	Fetal Intestine Large	intestine
10	chr10:44069200-44070600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr10:44069200-44070600	Active TSS	NH-A	brain
12	chr10:44069200-44070800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr10:44069200-44070800	Active TSS	Fetal Brain Male	brain
14	chr10:44069200-44070800	Bivalent/Poised TSS	NHEK	skin
15	chr10:44069400-44070600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr10:44069400-44070600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr10:44069400-44070600	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr10:44069400-44070600	Active TSS	Fetal Lung	lung
19	chr10:44069400-44070800	Active TSS	Brain Angular Gyrus	brain
20	chr10:44069400-44070800	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr10:44069400-44070800	Active TSS	Rectal Smooth Muscle	rectum
22	chr10:44069400-44071000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
23	chr10:44069600-44070600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr10:44069600-44070600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr10:44069600-44070600	Active TSS	HSMMtube	muscle
26	chr10:44069600-44070800	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr10:44069600-44070800	Active TSS	Brain Cingulate Gyrus	brain
28	chr10:44069600-44070800	Active TSS	Brain Hippocampus Middle	brain
29	chr10:44069800-44070600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr10:44069800-44070600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr10:44069800-44070600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
32	chr10:44069800-44070600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
33	chr10:44070000-44071000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr10:44070000-44071200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
35	chr10:44070200-44070600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr10:44070200-44070600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:44070200-44070600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
38	chr10:44070200-44070600	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr10:44070200-44070600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr10:44070200-44070600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr10:44070200-44070600	Active TSS	Colonic Mucosa	Colon
42	chr10:44070200-44070600	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr10:44070200-44070600	Enhancers	Pancreas	Pancrea
44	chr10:44070200-44070600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr10:44070200-44070600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr10:44070200-44070600	Flanking Active TSS	Osteobl	bone
47	chr10:44070200-44070800	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr10:44070200-44070800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr10:44070200-44070800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr10:44070200-44070800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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