Variant report

Variant	rs3743470
Chromosome Location	chr15:93425541-93425542
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	MAX	chr15:93425431-93426225	K562	blood:	n/a	n/a
2	CTCF	chr15:93425400-93425550	NHDF-neo	bronchial:	n/a	n/a
3	JUND	chr15:93425313-93426815	A549	lung:	n/a	chr15:93426771-93426779
4	RCOR1	chr15:93425182-93426534	HepG2	liver:	n/a	n/a
5	EP300	chr15:93425048-93426248	T-47D	breast:	n/a	chr15:93425381-93425391 chr15:93425408-93425422
6	EGR1	chr15:93425399-93426125	K562	blood:	n/a	chr15:93426006-93426020
7	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
8	TBL1XR1	chr15:93425264-93426224	K562	blood:	n/a	n/a
9	RELA	chr15:93425121-93426173	GM19099	blood:	n/a	n/a
10	ZC3H11A	chr15:93424871-93426167	K562	blood:	n/a	n/a
11	TAF1	chr15:93425424-93426243	PFSK-1	brain:	n/a	n/a
12	ELF1	chr15:93425371-93426119	HepG2	liver:	n/a	n/a
13	POLR2A	chr15:93424491-93428698	GM12891	blood:	n/a	n/a
14	SIN3A	chr15:93425260-93428319	H1-hESC	embryonic stem cell:	n/a	n/a
15	MYC	chr15:93425524-93426053	MCF10A-Er-Src	breast:	n/a	n/a
16	REST	chr15:93424890-93425702	A549	lung:	n/a	chr15:93425104-93425118
17	PBX3	chr15:93425165-93426209	SK-N-SH	brain:	n/a	chr15:93425396-93425405
18	SRF	chr15:93425436-93425871	HepG2	liver:	n/a	n/a
19	JUND	chr15:93425166-93425736	HepG2	liver:	n/a	n/a
20	BHLHE40	chr15:93425100-93426159	K562	blood:	n/a	n/a
21	POLR2A	chr15:93424993-93426703	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr15:93424514-93426185	U87	brain:	n/a	n/a
23	STAT5A	chr15:93425032-93425792	GM12878	blood:	n/a	chr15:93425763-93425771
24	POU2F2	chr15:93425080-93426229	GM12891	blood:	n/a	n/a
25	RAD21	chr15:93425197-93426199	Hela-S3	cervix:	n/a	chr15:93426068-93426077
26	YY1	chr15:93425250-93426416	H1-hESC	embryonic stem cell:	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
27	TAF1	chr15:93425297-93426243	SK-N-SH	brain:	n/a	n/a
28	ZNF384	chr15:93425259-93425743	GM12878	blood:	n/a	n/a
29	MAX	chr15:93425341-93426313	ECC-1	luminal epithelium:	n/a	n/a
30	CHD2	chr15:93425220-93426177	K562	blood:	n/a	chr15:93426003-93426013
31	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
32	POLR2A	chr15:93425034-93426761	K562	blood:	n/a	n/a
33	EBF1	chr15:93425166-93426102	GM12878	blood:	n/a	n/a
34	IRF3	chr15:93425515-93425890	GM12878	blood:	n/a	chr15:93425619-93425628
35	STAT3	chr15:93425511-93425779	MCF10A-Er-Src	breast:	n/a	chr15:93425763-93425771
36	POLR2A	chr15:93424986-93428747	GM12878	blood:	n/a	n/a
37	ELF1	chr15:93425390-93426640	GM12878	blood:	n/a	n/a
38	ELF1	chr15:93425380-93425887	A549	lung:	n/a	n/a
39	EP300	chr15:93425052-93426135	GM12878	blood:	n/a	chr15:93425381-93425391 chr15:93425408-93425422
40	POLR2A	chr15:93424787-93425776	U87	brain:	n/a	n/a
41	SIN3A	chr15:93425367-93426617	GM12878	blood:	n/a	n/a
42	FOXA1	chr15:93425116-93425863	HepG2	liver:	n/a	n/a
43	ZMIZ1	chr15:93424784-93426272	K562	blood:	n/a	n/a
44	TEAD4	chr15:93424718-93426192	K562	blood:	n/a	n/a
45	YY1	chr15:93425361-93426274	GM12891	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
46	YY1	chr15:93425453-93426259	NT2-D1	testis:	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
47	POLR2A	chr15:93425074-93428806	H1-neurons	neurons:	n/a	n/a
48	REST	chr15:93424836-93430889	H1-neurons	neurons:	n/a	chr15:93425104-93425118
49	TAF1	chr15:93425127-93426297	A549	lung:	n/a	n/a
50	TAF1	chr15:93425053-93425860	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:93352108..93352936-chr15:93425171..93425678,2	K562	blood:
2	chr14:24740252..24740952-chr15:93425313..93426012,2	Hela-S3	cervix:
3	chr11:18548153..18548751-chr15:93425186..93425734,2	Hela-S3	cervix:
4	chr1:186648896..186649559-chr15:93425048..93425747,2	Hela-S3	cervix:
5	chr11:62607333..62609223-chr15:93424710..93426737,2	K562	blood:
6	chr11:118991887..118992547-chr15:93425189..93426017,2	NB4	blood:
7	chr15:93333327..93367027-chr15:93419774..93462750,363	K562	blood:
8	chr15:93339450..93342002-chr15:93423524..93425580,2	MCF-7	breast:
9	chr15:93425198..93426173-chr6:74230195..74230813,2	Hela-S3	cervix:
10	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
11	chr15:93425116..93426959-chr6:26041379..26043913,2	MCF-7	breast:
12	chr12:57082176..57083030-chr15:93425152..93425714,2	Hela-S3	cervix:
13	chr15:93352256..93353063-chr15:93425255..93425934,3	Hela-S3	cervix:
14	chr15:93425219..93426130-chr7:99613026..99613921,3	Hela-S3	cervix:
15	chr15:93425070..93425680-chr9:33264389..33265229,2	HCT-116	colon:
16	chr15:69743883..69746535-chr15:93425105..93427133,2	MCF-7	breast:
17	chr15:93424784..93426792-chr15:93481094..93482707,2	MCF-7	breast:
18	chr15:93412399..93413366-chr15:93424771..93425883,5	MCF-7	breast:
19	chr15:93337836..93370220-chr15:93420085..93452591,332	K562	blood:
20	chr15:93345383..93371459-chr15:93416796..93454653,318	MCF-7	breast:
21	chr15:59040871..59041490-chr15:93425219..93425886,2	Hela-S3	cervix:
22	chr15:93424876..93427339-chr17:58154118..58156433,2	MCF-7	breast:
23	chr1:43282650..43283493-chr15:93425433..93425937,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000272888	TF binding region
CHD2	TF binding region
ENSG00000196226	Chromatin interaction
ENSG00000258527	Chromatin interaction
ENSG00000100949	Chromatin interaction
ENSG00000107262	Chromatin interaction
ENSG00000173575	Chromatin interaction
ENSG00000164010	Chromatin interaction
ENSG00000177868	Chromatin interaction
ENSG00000068097	Chromatin interaction
ENSG00000172273	Chromatin interaction
ENSG00000086065	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000258922	Chromatin interaction
ENSG00000185442	Chromatin interaction
ENSG00000137818	Chromatin interaction
ENSG00000073756	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000074319	Chromatin interaction
ENSG00000137845	Chromatin interaction
ENSG00000106261	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3743470	CHD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93421800-93426000	Weak transcription	Ovary	ovary
2	chr15:93422200-93426000	Weak transcription	Gastric	stomach
3	chr15:93423400-93425600	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr15:93423600-93425600	Enhancers	Spleen	Spleen
5	chr15:93424000-93425600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:93424000-93425600	Flanking Active TSS	K562	blood
7	chr15:93424200-93425600	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr15:93424200-93425600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr15:93424200-93425600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr15:93424200-93425600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr15:93424200-93425600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:93424200-93426000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:93424400-93425600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:93424400-93425600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr15:93424400-93425600	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr15:93424400-93425600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr15:93424400-93425600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:93424400-93425600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr15:93424400-93425600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:93424400-93425600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:93424400-93425600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:93424400-93425600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr15:93424400-93427000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:93424400-93430800	Active TSS	Aorta	Aorta
25	chr15:93424600-93425600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr15:93424600-93425600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr15:93424600-93425600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr15:93424600-93425600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr15:93424600-93425600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:93424600-93425600	Flanking Active TSS	Liver	Liver
31	chr15:93424600-93425600	Flanking Active TSS	Fetal Lung	lung
32	chr15:93424600-93425600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr15:93424600-93425600	Flanking Active TSS	HMEC	breast
34	chr15:93424600-93425600	Flanking Active TSS	NH-A	brain
35	chr15:93424600-93425600	Flanking Active TSS	Osteobl	bone
36	chr15:93424600-93429200	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr15:93424800-93425600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr15:93424800-93425600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr15:93424800-93425600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:93424800-93425600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr15:93424800-93425600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr15:93424800-93425600	Flanking Active TSS	Fetal Muscle Leg	muscle
43	chr15:93424800-93425600	Flanking Active TSS	Fetal Stomach	stomach
44	chr15:93424800-93425600	Flanking Active TSS	GM12878-XiMat	blood
45	chr15:93424800-93428600	Active TSS	Colonic Mucosa	Colon
46	chr15:93424800-93429400	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr15:93425000-93425600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr15:93425000-93425600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr15:93425000-93425600	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr15:93425000-93425600	Flanking Active TSS	Fetal Brain Male	brain

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