Variant report

Variant	rs554975390
Chromosome Location	chr15:93425200-93425201
allele	A/C
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	RCOR1	chr15:93425182-93426534	HepG2	liver:	n/a	n/a
2	EP300	chr15:93425048-93426248	T-47D	breast:	n/a	chr15:93425381-93425391 chr15:93425408-93425422
3	TFAP2A	chr15:93425194-93426696	Hela-S3	cervix:	n/a	chr15:93426645-93426656 chr15:93426645-93426657 chr15:93426169-93426180 chr15:93426646-93426661 chr15:93426566-93426577 chr15:93425631-93425639 chr15:93425631-93425639 chr15:93425631-93425639 chr15:93425629-93425640
4	RELA	chr15:93425121-93426173	GM19099	blood:	n/a	n/a
5	ZC3H11A	chr15:93424871-93426167	K562	blood:	n/a	n/a
6	ESR1	chr15:93425120-93425445	T-47D	breast:	n/a	n/a
7	POLR2A	chr15:93424491-93428698	GM12891	blood:	n/a	n/a
8	REST	chr15:93424890-93425702	A549	lung:	n/a	chr15:93425104-93425118
9	PBX3	chr15:93425165-93426209	SK-N-SH	brain:	n/a	chr15:93425396-93425405
10	JUND	chr15:93425166-93425736	HepG2	liver:	n/a	n/a
11	BHLHE40	chr15:93425100-93426159	K562	blood:	n/a	n/a
12	POLR2A	chr15:93424993-93426703	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr15:93424514-93426185	U87	brain:	n/a	n/a
14	STAT5A	chr15:93425032-93425792	GM12878	blood:	n/a	chr15:93425763-93425771
15	CTCF	chr15:93425200-93425350	HBMEC	blood vessel:	n/a	n/a
16	POU2F2	chr15:93425080-93426229	GM12891	blood:	n/a	n/a
17	RAD21	chr15:93425197-93426199	Hela-S3	cervix:	n/a	chr15:93426068-93426077
18	YY1	chr15:93425141-93426283	GM12892	blood:	n/a	chr15:93426071-93426079 chr15:93425973-93425993 chr15:93425976-93425998 chr15:93426069-93426077 chr15:93425979-93425987 chr15:93426070-93426080 chr15:93425974-93425993 chr15:93426182-93426193 chr15:93426063-93426082
19	POLR2A	chr15:93425034-93426761	K562	blood:	n/a	n/a
20	EBF1	chr15:93425166-93426102	GM12878	blood:	n/a	n/a
21	POLR2A	chr15:93424986-93428747	GM12878	blood:	n/a	n/a
22	EP300	chr15:93425052-93426135	GM12878	blood:	n/a	chr15:93425381-93425391 chr15:93425408-93425422
23	POLR2A	chr15:93424787-93425776	U87	brain:	n/a	n/a
24	FOXA1	chr15:93425116-93425863	HepG2	liver:	n/a	n/a
25	ZMIZ1	chr15:93424784-93426272	K562	blood:	n/a	n/a
26	TEAD4	chr15:93424718-93426192	K562	blood:	n/a	n/a
27	POLR2A	chr15:93425074-93428806	H1-neurons	neurons:	n/a	n/a
28	REST	chr15:93424836-93430889	H1-neurons	neurons:	n/a	chr15:93425104-93425118
29	TAF1	chr15:93425127-93426297	A549	lung:	n/a	n/a
30	TAF1	chr15:93425053-93425860	MCF-7	breast:	n/a	n/a
31	POLR2A	chr15:93424935-93426746	GM18526	blood:	n/a	n/a
32	POLR2A	chr15:93425165-93428729	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr15:93424349-93427371	GM12878	blood:	n/a	n/a
34	MYC	chr15:93424553-93426652	K562	blood:	n/a	n/a
35	POLR2A	chr15:93424751-93425824	SK-N-MC	brain:	n/a	n/a
36	TAF1	chr15:93425132-93426239	H1-neurons	neurons:	n/a	n/a
37	TBP	chr15:93425168-93426204	Hela-S3	cervix:	n/a	n/a
38	NFATC1	chr15:93424857-93425790	GM12878	blood:	n/a	n/a
39	POLR2A	chr15:93424642-93426415	PFSK-1	brain:	n/a	n/a
40	POLR2A	chr15:93425193-93426500	Gliobla	brain:	n/a	n/a
41	POLR2A	chr15:93424911-93427251	HL-60	blood:	n/a	n/a
42	GTF2F1	chr15:93425195-93426184	Hela-S3	cervix:	n/a	n/a
43	IRF1	chr15:93424557-93426511	K562	blood:	n/a	chr15:93424872-93424882 chr15:93425619-93425628 chr15:93424871-93424882 chr15:93424762-93424773 chr15:93424763-93424777 chr15:93424763-93424773 chr15:93424759-93424773 chr15:93424864-93424876 chr15:93424964-93424971 chr15:93425413-93425423 chr15:93424868-93424882 chr15:93424757-93424774 chr15:93425409-93425423
44	SP1	chr15:93425065-93426318	HCT-116	colon:	n/a	chr15:93425998-93426007 chr15:93426000-93426014 chr15:93425704-93425715 chr15:93426006-93426020 chr15:93425701-93425715 chr15:93425997-93426006 chr15:93426003-93426017 chr15:93425996-93426008 chr15:93425730-93425751 chr15:93425618-93425639
45	ZNF143	chr15:93424770-93426199	K562	blood:	n/a	chr15:93425999-93426017
46	POLR2A	chr15:93424850-93425717	GM12891	blood:	n/a	n/a
47	MXI1	chr15:93424871-93427275	IMR90	lung:	n/a	chr15:93425142-93425157
48	POLR2A	chr15:93424974-93425779	GM12891	blood:	n/a	n/a
49	POLR2A	chr15:93424905-93425892	H1-hESC	embryonic stem cell:	n/a	n/a
50	EP300	chr15:93424821-93426198	A549	lung:	n/a	chr15:93424934-93424948 chr15:93425381-93425391 chr15:93425408-93425422

No.	Distal block	Cell Line	Cell type
1	chr15:93352108..93352936-chr15:93425171..93425678,2	K562	blood:
2	chr11:18548153..18548751-chr15:93425186..93425734,2	Hela-S3	cervix:
3	chr1:186648896..186649559-chr15:93425048..93425747,2	Hela-S3	cervix:
4	chr11:62607333..62609223-chr15:93424710..93426737,2	K562	blood:
5	chr11:118991887..118992547-chr15:93425189..93426017,2	NB4	blood:
6	chr15:93333327..93367027-chr15:93419774..93462750,363	K562	blood:
7	chr15:93339450..93342002-chr15:93423524..93425580,2	MCF-7	breast:
8	chr15:93425198..93426173-chr6:74230195..74230813,2	Hela-S3	cervix:
9	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
10	chr15:93425116..93426959-chr6:26041379..26043913,2	MCF-7	breast:
11	chr12:57082176..57083030-chr15:93425152..93425714,2	Hela-S3	cervix:
12	chr15:93425070..93425680-chr9:33264389..33265229,2	HCT-116	colon:
13	chr15:69743883..69746535-chr15:93425105..93427133,2	MCF-7	breast:
14	chr15:93424784..93426792-chr15:93481094..93482707,2	MCF-7	breast:
15	chr15:93412399..93413366-chr15:93424771..93425883,5	MCF-7	breast:
16	chr15:93337836..93370220-chr15:93420085..93452591,332	K562	blood:
17	chr15:93345383..93371459-chr15:93416796..93454653,318	MCF-7	breast:
18	chr15:93424876..93427339-chr17:58154118..58156433,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272888	TF binding region
CHD2	TF binding region
ENSG00000258922	Chromatin interaction
ENSG00000258527	Chromatin interaction
ENSG00000068097	Chromatin interaction
ENSG00000107262	Chromatin interaction
ENSG00000073756	Chromatin interaction
ENSG00000185442	Chromatin interaction
ENSG00000172273	Chromatin interaction
ENSG00000196226	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000137818	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000074319	Chromatin interaction
ENSG00000173575	Chromatin interaction
ENSG00000086065	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
3	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
4	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
5	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv1047496	chr15:93412778-93475878	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1036560	chr15:93413594-93462163	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
8	esv3420117	chr15:93423948-93428546	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	esv3424005	chr15:93424973-93427821	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:150 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93413600-93425200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:93413800-93425200	Weak transcription	Left Ventricle	heart
3	chr15:93420000-93425200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr15:93420400-93425200	Weak transcription	Psoas Muscle	Psoas
5	chr15:93421400-93425200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:93421800-93425200	Enhancers	Placenta	Placenta
7	chr15:93421800-93426000	Weak transcription	Ovary	ovary
8	chr15:93422000-93425200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:93422200-93425200	Weak transcription	Right Ventricle	heart
10	chr15:93422200-93426000	Weak transcription	Gastric	stomach
11	chr15:93423200-93425200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr15:93423200-93425200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:93423400-93425400	Flanking Active TSS	Dnd41	blood
14	chr15:93423400-93425600	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr15:93423600-93425400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr15:93423600-93425400	Flanking Active TSS	Fetal Thymus	thymus
17	chr15:93423600-93425600	Enhancers	Spleen	Spleen
18	chr15:93423800-93425200	Enhancers	Fetal Intestine Small	intestine
19	chr15:93423800-93425200	Weak transcription	Small Intestine	intestine
20	chr15:93423800-93425400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:93424000-93425200	Enhancers	Fetal Intestine Large	intestine
22	chr15:93424000-93425400	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr15:93424000-93425400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr15:93424000-93425600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:93424000-93425600	Flanking Active TSS	K562	blood
26	chr15:93424200-93425200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr15:93424200-93425200	Enhancers	Stomach Mucosa	stomach
28	chr15:93424200-93425400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:93424200-93425400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:93424200-93425400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:93424200-93425400	Flanking Active TSS	A549	lung
32	chr15:93424200-93425400	Flanking Active TSS	NHEK	skin
33	chr15:93424200-93425600	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr15:93424200-93425600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr15:93424200-93425600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr15:93424200-93425600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr15:93424200-93425600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:93424200-93426000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr15:93424400-93425400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:93424400-93425400	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr15:93424400-93425400	Flanking Active TSS	Fetal Brain Female	brain
42	chr15:93424400-93425400	Flanking Active TSS	Fetal Kidney	kidney
43	chr15:93424400-93425600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:93424400-93425600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr15:93424400-93425600	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr15:93424400-93425600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
47	chr15:93424400-93425600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:93424400-93425600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr15:93424400-93425600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:93424400-93425600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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