Variant report

Variant	rs11252089
Chromosome Location	chr10:3824084-3824085
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	chr10:3823661-3828444	HepG2	liver:	n/a	chr10:3824435-3824450 chr10:3824437-3824452
2	POLR2A	chr10:3819924-3827450	U87	brain:	n/a	n/a
3	MXI1	chr10:3822375-3828474	GM12878	blood:	n/a	chr10:3824435-3824450 chr10:3824437-3824452
4	POLR2A	chr10:3818907-3829564	HUVEC	blood vessel:	n/a	n/a
5	CTCF	chr10:3824020-3824170	AG04450	lung:	n/a	n/a
6	POLR2A	chr10:3821276-3829243	Hela-S3	cervix:	n/a	n/a
7	MAX	chr10:3823661-3824259	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr10:3820104-3829210	GM12891	blood:	n/a	n/a
9	POLR2A	chr10:3823250-3824356	HL-60	blood:	n/a	n/a
10	BHLHE40	chr10:3822796-3828732	GM12878	blood:	n/a	chr10:3824428-3824437 chr10:3827945-3827961 chr10:3824423-3824444 chr10:3824429-3824438 chr10:3824429-3824438
11	POLR2A	chr10:3819960-3825896	K562	blood:	n/a	n/a
12	POLR2A	chr10:3823702-3824193	HepG2	liver:	n/a	n/a
13	SPI1	chr10:3823387-3824137	GM12878	blood:	n/a	n/a
14	RAD21	chr10:3824070-3824437	SK-N-SH_RA	brain:	n/a	n/a
15	POLR2A	chr10:3814705-3830204	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr10:3820673-3829213	HepG2	liver:	n/a	n/a
17	POLR2A	chr10:3823648-3825889	GM12878	blood:	n/a	n/a
18	RAD21	chr10:3823436-3829101	SK-N-SH	brain:	n/a	n/a
19	RAD21	chr10:3823525-3824516	SK-N-SH_RA	brain:	n/a	n/a
20	TBL1XR1	chr10:3823284-3828535	GM12878	blood:	n/a	n/a
21	POLR2A	chr10:3820065-3829734	GM12878	blood:	n/a	n/a
22	CHD1	chr10:3823060-3828929	GM12878	blood:	n/a	chr10:3827827-3827837
23	RAD21	chr10:3823294-3829439	IMR90	lung:	n/a	chr10:3829319-3829328
24	PBX3	chr10:3824080-3825925	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr10:3814486-3830042	IMR90	lung:	n/a	n/a
26	TCF12	chr10:3823611-3826518	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr10:3823571-3828990	GM15510	blood:	n/a	n/a
28	POLR2A	chr10:3823636-3827492	H1-hESC	embryonic stem cell:	n/a	n/a
29	GATA3	chr10:3823078-3826602	SK-N-SH	brain:	n/a	chr10:3824498-3824507 chr10:3825263-3825272 chr10:3825009-3825019
30	RAD21	chr10:3823503-3824422	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr10:3819915-3829166	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr10:3820127-3829261	GM12891	blood:	n/a	n/a
33	POLR2A	chr10:3819959-3829547	GM12891	blood:	n/a	n/a
34	POLR2A	chr10:3819944-3829311	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr10:3821000-3829231	GM12892	blood:	n/a	n/a
36	POLR2A	chr10:3821418-3829270	GM19193	blood:	n/a	n/a
37	RCOR1	chr10:3823143-3826747	GM12878	blood:	n/a	n/a
38	POLR2A	chr10:3819984-3830280	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr10:3823006-3829288	ProgFib	skin:	n/a	n/a
40	POLR2A	chr10:3814512-3830383	HepG2	liver:	n/a	n/a
41	POLR2A	chr10:3823657-3824215	GM12878	blood:	n/a	n/a
42	POLR2A	chr10:3815794-3829347	GM18505	blood:	n/a	n/a
43	POLR2A	chr10:3823129-3829267	PFSK-1	brain:	n/a	n/a
44	WRNIP1	chr10:3821512-3827000	GM12878	blood:	n/a	n/a
45	POLR2A	chr10:3814609-3830233	HUVEC	blood vessel:	n/a	n/a
46	CHD1	chr10:3815594-3829758	IMR90	lung:	n/a	chr10:3827827-3827837
47	POLR2A	chr10:3823585-3824094	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr10:3821046-3826536	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr10:3819946-3829202	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr10:3824021-3825827	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:3820450..3836478-chr10:3861249..3889254,84	K562	blood:
2	chr10:3822661..3831329-chr10:3860829..3877795,40	MCF-7	breast:
3	chr10:3823775..3824695-chr15:65596871..65597443,2	Hela-S3	cervix:
4	chr10:3297823..3299622-chr10:3823374..3826343,2	MCF-7	breast:

Variant related genes	Relation type
KLF6	TF binding region
ENSG00000226762	Chromatin interaction
ENSG00000230573	Chromatin interaction
ENSG00000200156	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs2025681	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043680	chr10:3551191-4038002	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv540447	chr10:3777819-3847629	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv1048831	chr10:3792130-3825343	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1035650	chr10:3795359-3830207	Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv540448	chr10:3804336-3830075	Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv540449	chr10:3804336-3833414	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv540450	chr10:3804336-3859639	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv540451	chr10:3804336-3868002	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
9	nsv540452	chr10:3811996-3830075	Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv540453	chr10:3811996-3847629	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
11	nsv540454	chr10:3820854-3833414	Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	45 gene(s)	inside rSNPs	n/a
12	nsv540455	chr10:3820854-3847629	Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	46 gene(s)	inside rSNPs	n/a
13	nsv540456	chr10:3820854-3868002	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	n/a
14	nsv540457	chr10:3822531-3847629	Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	46 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:3817600-3824600	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
2	chr10:3817800-3827400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr10:3818000-3824800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
4	chr10:3818200-3826200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
5	chr10:3819200-3824400	Strong transcription	H9 Cell Line	embryonic stem cell
6	chr10:3819200-3826600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr10:3819400-3824400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
8	chr10:3819400-3824800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr10:3819400-3825200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
10	chr10:3819400-3826200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr10:3819400-3826800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
12	chr10:3819600-3824200	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr10:3819600-3824400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr10:3819600-3824400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr10:3819800-3824400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr10:3820200-3824400	Transcr. at gene 5' and 3'	Right Ventricle	heart
17	chr10:3820200-3824400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
18	chr10:3820200-3824800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr10:3820200-3825000	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
20	chr10:3820200-3825000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
21	chr10:3820200-3825200	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
22	chr10:3820200-3826400	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr10:3820200-3826400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr10:3820200-3826400	Transcr. at gene 5' and 3'	Osteobl	bone
25	chr10:3820200-3827200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:3820200-3827200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
27	chr10:3820200-3827400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
28	chr10:3820200-3827400	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
29	chr10:3820400-3824200	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
30	chr10:3820400-3824200	Transcr. at gene 5' and 3'	HSMMtube	muscle
31	chr10:3820400-3824600	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
32	chr10:3820400-3824800	Transcr. at gene 5' and 3'	HMEC	breast
33	chr10:3820400-3825000	Transcr. at gene 5' and 3'	NH-A	brain
34	chr10:3820400-3826400	Transcr. at gene 5' and 3'	NHLF	lung
35	chr10:3820400-3826800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr10:3820400-3827000	Transcr. at gene 5' and 3'	NHEK	skin
37	chr10:3820600-3826600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr10:3820800-3824200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr10:3820800-3824400	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
40	chr10:3820800-3825000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr10:3821000-3824600	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
42	chr10:3821000-3824600	Transcr. at gene 5' and 3'	HSMM	muscle
43	chr10:3821000-3825000	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
44	chr10:3821000-3825000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
45	chr10:3821000-3827200	Transcr. at gene 5' and 3'	Dnd41	blood
46	chr10:3821200-3824400	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
47	chr10:3821200-3824400	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
48	chr10:3821200-3824800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr10:3821200-3825200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
50	chr10:3821400-3824200	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived

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