Variant report

Variant	rs541422430
Chromosome Location	chr10:22629544-22629545
allele	C/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	ZNF143	chr10:22629242-22629802	Hela-S3	cervix:	n/a	chr10:22629645-22629655
2	POLR2A	chr10:22629293-22630352	A549	lung:	n/a	n/a
3	POLR2A	chr10:22629109-22630192	HCT-116	colon:	n/a	n/a
4	RCOR1	chr10:22628910-22630409	K562	blood:	n/a	n/a
5	MAX	chr10:22628764-22630580	A549	lung:	n/a	chr10:22629645-22629655
6	ZMIZ1	chr10:22629114-22630181	K562	blood:	n/a	n/a
7	CCNT2	chr10:22629104-22630607	K562	blood:	n/a	chr10:22629697-22629706
8	SIN3AK20	chr10:22629261-22630076	K562	blood:	n/a	n/a
9	NFIC	chr10:22628910-22629900	SK-N-SH	brain:	n/a	n/a
10	RAD21	chr10:22629218-22629980	IMR90	lung:	n/a	chr10:22629720-22629734 chr10:22629721-22629735
11	CREB1	chr10:22628990-22630192	GM12878	blood:	n/a	n/a
12	MAX	chr10:22628984-22630393	ECC-1	luminal epithelium:	n/a	chr10:22629645-22629655
13	BCLAF1	chr10:22629133-22629972	GM12878	blood:	n/a	chr10:22629788-22629797 chr10:22629529-22629542
14	MAZ	chr10:22628921-22630448	IMR90	lung:	n/a	chr10:22629645-22629655
15	TCF12	chr10:22628927-22629778	A549	lung:	n/a	n/a
16	CTCF	chr10:22629460-22629610	SK-N-SH_RA	brain:	n/a	n/a
17	STAT3	chr10:22628897-22629559	MCF10A-Er-Src	breast:	n/a	n/a
18	RAD21	chr10:22629397-22629773	K562	blood:	n/a	chr10:22629720-22629734 chr10:22629721-22629735
19	POLR2A	chr10:22629230-22630349	HepG2	liver:	n/a	n/a
20	POLR2A	chr10:22628952-22630670	GM12891	blood:	n/a	n/a
21	CHD2	chr10:22629042-22629857	K562	blood:	n/a	chr10:22629793-22629800
22	MYC	chr10:22629497-22630302	MCF-7	breast:	n/a	chr10:22629645-22629655
23	STAT1	chr10:22629091-22629634	GM12878	blood:	n/a	n/a
24	CUX1	chr10:22628745-22629563	GM12878	blood:	n/a	n/a
25	TAF1	chr10:22629024-22630119	K562	blood:	n/a	n/a
26	REST	chr10:22629238-22630343	K562	blood:	n/a	chr10:22629884-22629897 chr10:22630191-22630211 chr10:22630195-22630208 chr10:22629882-22629892
27	POLR2A	chr10:22628988-22629652	U87	brain:	n/a	n/a
28	POLR2A	chr10:22629121-22629595	SK-N-MC	brain:	n/a	n/a
29	POLR2A	chr10:22629183-22630516	GM18526	blood:	n/a	n/a
30	ELF1	chr10:22629122-22630211	GM12878	blood:	n/a	chr10:22629603-22629615
31	ELK4	chr10:22629387-22629693	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr10:22629290-22629592	HL-60	blood:	n/a	n/a
33	TCF7L2	chr10:22629238-22630488	HCT-116	colon:	n/a	n/a
34	POU2F2	chr10:22629123-22629633	GM12878	blood:	n/a	chr10:22629460-22629472
35	YY1	chr10:22629264-22630052	GM12892	blood:	n/a	chr10:22629878-22629892 chr10:22629874-22629885 chr10:22629376-22629390 chr10:22629776-22629787 chr10:22629650-22629664 chr10:22629695-22629706
36	NFIC	chr10:22628858-22629727	GM12878	blood:	n/a	n/a
37	CHD1	chr10:22629448-22629635	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr10:22629156-22630060	GM12892	blood:	n/a	n/a
39	EP300	chr10:22628995-22629652	K562	blood:	n/a	n/a
40	SMARCB1	chr10:22629297-22630532	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr10:22629196-22629579	HUVEC	blood vessel:	n/a	n/a
42	ELF1	chr10:22629265-22630436	GM12878	blood:	n/a	chr10:22629603-22629615
43	HEY1	chr10:22628891-22630504	K562	blood:	n/a	chr10:22629645-22629660 chr10:22629654-22629669 chr10:22629534-22629549 chr10:22629609-22629624
44	RCOR1	chr10:22629030-22629960	GM12878	blood:	n/a	n/a
45	CTBP2	chr10:22629300-22630502	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr10:22629183-22630464	GM12892	blood:	n/a	n/a
47	POLR2A	chr10:22629168-22630610	GM12878	blood:	n/a	n/a
48	ETS1	chr10:22629314-22629666	K562	blood:	n/a	chr10:22629646-22629657
49	HCFC1	chr10:22629070-22630507	K562	blood:	n/a	n/a
50	TAF1	chr10:22629153-22630156	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:22290966..22293742-chr10:22628058..22631636,3	MCF-7	breast:
2	chr10:22603818..22606688-chr10:22628346..22630666,3	MCF-7	breast:
3	chr10:22629489..22630407-chr17:30676764..30677278,2	Hela-S3	cervix:
4	chr10:22629399..22631844-chr10:22647631..22650526,2	MCF-7	breast:
5	chr10:22628552..22630846-chr8:144350757..144353211,2	MCF-7	breast:
6	chr10:22625398..22631647-chr10:22676300..22682265,8	K562	blood:
7	chr10:22608172..22617536-chr10:22624000..22632852,24	MCF-7	breast:
8	chr10:22628696..22632444-chr10:22679412..22682265,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIP4K2A-3	chr10:22629306-22629544	ENSG00000272366.1

Variant related genes	Relation type
ENSG00000272366	TF binding region
SPAG6	TF binding region
ENSG00000148444	Chromatin interaction
ENSG00000136770	Chromatin interaction
ENSG00000077327	Chromatin interaction
ENSG00000269897	Chromatin interaction
ENSG00000168283	Chromatin interaction
ENSG00000207928	Chromatin interaction
ENSG00000233451	Chromatin interaction
ENSG00000010244	Chromatin interaction
ENSG00000108666	Chromatin interaction
ENSG00000250571	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv825292	chr10:22560347-22642200	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv825293	chr10:22575226-22637618	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv825294	chr10:22590627-22644910	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv825295	chr10:22591275-22643207	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv825296	chr10:22591339-22638994	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv894950	chr10:22591830-22639903	Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv894955	chr10:22594765-22631256	Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv894956	chr10:22594765-22633193	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv894957	chr10:22594765-22637381	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	esv1816646	chr10:22594765-22639707	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv894958	chr10:22594765-22639903	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv825297	chr10:22596793-22637576	Bivalent Enhancer Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv825299	chr10:22596793-22638994	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv550207	chr10:22605112-22631256	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	esv3512115	chr10:22628355-22629590	Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
16	esv3512116	chr10:22628355-22629590	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:22628800-22629600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
2	chr10:22628800-22629600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr10:22628800-22629600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
4	chr10:22628800-22629600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr10:22628800-22629600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr10:22628800-22630000	Active TSS	HMEC	breast
7	chr10:22628800-22630200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr10:22628800-22630200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr10:22628800-22630200	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr10:22628800-22630200	Active TSS	Brain Substantia Nigra	brain
11	chr10:22628800-22630200	Active TSS	Placenta Amnion	Placenta Amnion
12	chr10:22628800-22630400	Active TSS	Brain Angular Gyrus	brain
13	chr10:22628800-22630400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr10:22628800-22630400	Active TSS	HSMMtube	muscle
15	chr10:22628800-22630600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr10:22628800-22630600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr10:22628800-22630600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
18	chr10:22628800-22630600	Active TSS	Psoas Muscle	Psoas
19	chr10:22628800-22630800	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr10:22629000-22629600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
21	chr10:22629000-22629600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr10:22629000-22630000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr10:22629000-22630000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
24	chr10:22629000-22630000	Active TSS	Colonic Mucosa	Colon
25	chr10:22629000-22630000	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr10:22629000-22630000	Active TSS	Stomach Smooth Muscle	stomach
27	chr10:22629000-22630200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr10:22629000-22630200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr10:22629000-22630200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:22629000-22630400	Active TSS	Brain Hippocampus Middle	brain
31	chr10:22629000-22630400	Active TSS	A549	lung
32	chr10:22629000-22630600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr10:22629000-22630600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
34	chr10:22629000-22630600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr10:22629000-22630600	Active TSS	Aorta	Aorta
36	chr10:22629000-22630600	Active TSS	Ovary	ovary
37	chr10:22629000-22630600	Active TSS	Hela-S3	cervix
38	chr10:22629000-22630600	Active TSS	HSMM	muscle
39	chr10:22629000-22630800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr10:22629000-22631000	Active TSS	Right Atrium	heart
41	chr10:22629200-22629600	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr10:22629200-22629600	Active TSS	Primary hematopoietic stem cells	blood
43	chr10:22629200-22629600	Active TSS	Dnd41	blood
44	chr10:22629200-22629800	Bivalent/Poised TSS	Primary T helper naive cells from peripheral blood	blood
45	chr10:22629200-22630000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr10:22629200-22630000	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr10:22629200-22630000	Active TSS	Primary B cells from cord blood	blood
48	chr10:22629200-22630000	Active TSS	Primary B cells from peripheral blood	blood
49	chr10:22629200-22630000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr10:22629200-22630000	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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