Variant report

Variant	rs3743230
Chromosome Location	chr15:72669077-72669078
allele	C/T
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	TAF1	chr15:72667934-72669104	MCF-7	breast:	n/a	n/a
2	POLR2A	chr15:72667867-72669293	GM18505	blood:	n/a	n/a
3	GABPA	chr15:72667780-72669081	MCF-7	breast:	n/a	chr15:72668416-72668430
4	POLR2A	chr15:72667730-72669421	GM12891	blood:	n/a	n/a
5	ELF1	chr15:72667646-72669112	MCF-7	breast:	n/a	n/a
6	CHD1	chr15:72667866-72669102	GM12878	blood:	n/a	n/a
7	UBTF	chr15:72667892-72669125	K562	blood:	n/a	n/a
8	MAX	chr15:72667604-72669154	A549	lung:	n/a	chr15:72668396-72668407 chr15:72668396-72668405 chr15:72668346-72668355 chr15:72668395-72668408 chr15:72668395-72668408 chr15:72668397-72668406 chr15:72668345-72668356 chr15:72668397-72668406 chr15:72668395-72668408
9	MAZ	chr15:72667604-72669258	IMR90	lung:	n/a	chr15:72668396-72668407 chr15:72668396-72668405 chr15:72668346-72668355 chr15:72668395-72668408 chr15:72668395-72668408 chr15:72668397-72668406 chr15:72668345-72668356 chr15:72668397-72668406 chr15:72668395-72668408
10	POLR2A	chr15:72667729-72669683	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr15:72667794-72669169	GM19099	blood:	n/a	n/a
12	POLR2A	chr15:72667808-72669235	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr15:72667896-72669319	GM12878	blood:	n/a	n/a
14	WRNIP1	chr15:72667926-72669270	GM12878	blood:	n/a	n/a
15	USF2	chr15:72667710-72669679	Hela-S3	cervix:	n/a	chr15:72668397-72668406 chr15:72668361-72668372 chr15:72668398-72668407 chr15:72668397-72668406 chr15:72668344-72668355 chr15:72668391-72668412 chr15:72668396-72668407 chr15:72668395-72668408
16	GABPA	chr15:72667794-72669098	A549	lung:	n/a	chr15:72668416-72668430
17	POLR2A	chr15:72667544-72669257	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr15:72667870-72669403	HepG2	liver:	n/a	n/a
19	POLR2A	chr15:72667695-72669414	MCF10A-Er-Src	breast:	n/a	n/a
20	TBL1XR1	chr15:72668231-72669207	K562	blood:	n/a	n/a
21	MAX	chr15:72667841-72669080	A549	lung:	n/a	chr15:72668396-72668407 chr15:72668396-72668405 chr15:72668346-72668355 chr15:72668395-72668408 chr15:72668395-72668408 chr15:72668397-72668406 chr15:72668345-72668356 chr15:72668397-72668406 chr15:72668395-72668408
22	POLR2A	chr15:72667765-72669084	PBDE	blood:	n/a	n/a
23	POLR2A	chr15:72667694-72669396	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr15:72667912-72669081	GM12878	blood:	n/a	n/a
25	GTF2F1	chr15:72668088-72669167	Hela-S3	cervix:	n/a	n/a
26	MYC	chr15:72668192-72669097	H1-hESC	embryonic stem cell:	n/a	chr15:72668396-72668407 chr15:72668396-72668405 chr15:72668346-72668355 chr15:72668395-72668408 chr15:72668395-72668408 chr15:72668397-72668406 chr15:72668345-72668356 chr15:72668397-72668406 chr15:72668395-72668408
27	POLR2A	chr15:72667517-72669230	HepG2	liver:	n/a	n/a
28	SIN3AK20	chr15:72667588-72669257	MCF-7	breast:	n/a	n/a
29	POLR2A	chr15:72667882-72669275	K562	blood:	n/a	n/a
30	MXI1	chr15:72667585-72669642	SK-N-SH	brain:	n/a	chr15:72668398-72668407

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:72669047-72669097	HRE	kidney:	n/a
2	chr15:72669047-72669097	SAEC	small airway:	n/a
3	chr15:72669047-72669097	ProgFib	skin:	n/a
4	chr15:72669047-72669097	GM06990	blood:	n/a
5	chr15:72669047-72669097	NHBE	bronchial:	n/a
6	chr15:72669047-72669097	H1-hESC	embryonic stem cell:	embryo
7	chr15:72669047-72669097	AoSMC	blood vessel:	n/a
8	chr15:72669047-72669097	NB4	blood:	n/a
9	chr15:72669047-72669097	Caco-2	colon:	n/a
10	chr15:72669047-72669097	ovcar-3	ovarian:	n/a
11	chr15:72669047-72669097	MCF-7	breast:	n/a
12	chr15:72669047-72669097	HCT-116	colon:	n/a
13	chr15:72669047-72669097	HRPEpiC	eye:	n/a
14	chr15:72669047-72669097	AG10803	skin:	n/a
15	chr15:72669047-72669097	NH-A	brain:	n/a
16	chr15:72669047-72669097	HNPCEpiC	eye:	n/a
17	chr15:72669047-72669097	SKMC	muscle:	n/a
18	chr15:72669047-72669097	SK-N-MC	brain:	n/a
19	chr15:72669047-72669097	GM12892	blood:	n/a
20	chr15:72669047-72669097	HRCEpiC	kidney:	n/a
21	chr15:72669047-72669097	HepG2	liver:	n/a
22	chr15:72669047-72669097	RPTEC	kidney:	n/a
23	chr15:72669047-72669097	T-47D	breast:	n/a
24	chr15:72669047-72669097	GM19239	blood:	n/a
25	chr15:72669047-72669097	SK-N-SH	brain:	n/a
26	chr15:72669047-72669097	HPAEpiC	pulmonary alveolar:	n/a
27	chr15:72669047-72669097	HCF	heart:	n/a
28	chr15:72669047-72669097	CMK	blood:	n/a
29	chr15:72669047-72669097	AG04449	skin:	fetal
30	chr15:72669047-72669097	BJ	skin:	n/a
31	chr15:72669047-72669097	HL-60	blood:	n/a
32	chr15:72669047-72669097	HCM	heart:	n/a
33	chr15:72669047-72669097	NHDF-neo	bronchial:	n/a
34	chr15:72669047-72669097	A549	lung:	n/a
35	chr15:72669047-72669097	HUVEC	blood vessel:	n/a
36	chr15:72669047-72669097	HEEpiC	esophagus:	n/a
37	chr15:72669047-72669097	PANC-1	pancreas:	n/a
38	chr15:72669047-72669097	AG04450	lung:	fetal
39	chr15:72669047-72669097	HEK293	kidney:	embryo
40	chr15:72669047-72669097	AG09319	gingival:	n/a
41	chr15:72669047-72669097	MCF10A-Er-Src	breast:	n/a
42	chr15:72669047-72669097	K562	blood:	n/a
43	chr15:72669047-72669097	PrEC	prostate:	n/a
44	chr15:72669047-72669097	HCPEpiC	choroid plexus:	n/a
45	chr15:72669047-72669097	BE2_C	brain:	n/a
46	chr15:72669047-72669097	LNCaP	prostate:	n/a
47	chr15:72669047-72669097	GM12878	blood:	n/a
48	chr15:72669047-72669097	GM12891	blood:	n/a
49	chr15:72669047-72669097	HMEC	breast:	n/a
50	chr15:72669047-72669097	ECC-1	luminal epithelium:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:72666408..72669827-chr15:72764535..72767754,3	MCF-7	breast:
2	chr15:72667344..72672450-chr15:72764755..72768100,8	K562	blood:
3	chr15:72612273..72613953-chr15:72667924..72670021,2	K562	blood:
4	chr15:72521644..72524080-chr15:72668948..72670929,2	MCF-7	breast:
5	chr15:72669000..72671381-chr15:72700452..72702096,2	MCF-7	breast:
6	chr15:72666558..72670735-chr15:72765041..72769475,12	MCF-7	breast:
7	chr15:72667335..72670021-chr15:72670916..72672752,3	MCF-7	breast:
8	chr15:72561194..72564093-chr15:72666798..72669351,2	MCF-7	breast:
9	chr15:72518920..72521207-chr15:72667359..72669171,2	MCF-7	breast:
10	chr15:72668155..72670512-chr20:49346499..49348280,2	MCF-7	breast:
11	chr15:72668330..72669227-chr17:59476887..59477547,2	MCF-7	breast:
12	chr14:69259233..69260141-chr15:72668206..72669170,2	Hela-S3	cervix:

Variant related genes	Relation type
HEXA	TF binding region
ENSG00000260729	TF binding region
HEXA	CpG island
ENSG00000260729	CpG island
ENSG00000121068	Chromatin interaction
ENSG00000185650	Chromatin interaction
ENSG00000166233	Chromatin interaction
ENSG00000273025	Chromatin interaction
ENSG00000243007	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000140488	Chromatin interaction
ENSG00000137817	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000067225	Chromatin interaction
ENSG00000261423	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10518988	0.88[JPT][hapmap]
rs11072376	0.88[JPT][hapmap]
rs12900846	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16956866	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16956899	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16956988	0.84[ASW][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs1800430	1.00[ASW][hapmap];0.88[YRI][hapmap]
rs1972692	1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs2162236	1.00[CHD][hapmap]
rs2415135	0.88[JPT][hapmap]
rs2912216	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2912228	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2959913	0.87[ASN][1000 genomes]
rs57155740	0.82[ASN][1000 genomes]
rs58110372	0.82[ASN][1000 genomes]
rs60106752	0.82[ASN][1000 genomes]
rs60207997	0.82[ASN][1000 genomes]
rs7174307	0.82[ASN][1000 genomes]
rs7175437	0.82[ASN][1000 genomes]
rs73442522	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73442536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73442539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73442545	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73442549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73442560	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73442591	0.82[ASN][1000 genomes]
rs73442595	0.82[ASN][1000 genomes]
rs73444703	0.82[ASN][1000 genomes]
rs73444714	0.82[ASN][1000 genomes]
rs73444720	0.82[ASN][1000 genomes]
rs73444723	0.82[ASN][1000 genomes]
rs73444736	0.82[ASN][1000 genomes]
rs73444755	0.82[ASN][1000 genomes]
rs73444759	0.82[ASN][1000 genomes]
rs73444761	0.82[ASN][1000 genomes]
rs73444773	0.82[ASN][1000 genomes]
rs73444774	0.82[ASN][1000 genomes]
rs73444791	0.82[ASN][1000 genomes]
rs73444794	0.82[ASN][1000 genomes]
rs73444798	0.82[ASN][1000 genomes]
rs73444802	0.82[ASN][1000 genomes]
rs73446604	0.82[ASN][1000 genomes]
rs8025088	0.88[JPT][hapmap]
rs8026681	0.88[JPT][hapmap]
rs8031264	0.87[ASN][1000 genomes]
rs8032276	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs8035007	0.82[ASN][1000 genomes]
rs962407	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs9972606	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
3	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
4	nsv534037	chr15:72659210-72964029	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv521971	chr15:72666424-72678738	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72666600-72669200	Active TSS	Fetal Intestine Large	intestine
2	chr15:72666600-72669400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:72666800-72669400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:72667000-72669200	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr15:72667000-72669400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr15:72667000-72669400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:72667000-72669400	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr15:72667000-72669400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr15:72667200-72669200	Active TSS	H1 Cell Line	embryonic stem cell
10	chr15:72667200-72669200	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr15:72667200-72669200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr15:72667200-72669200	Active TSS	HSMMtube	muscle
13	chr15:72667200-72669400	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr15:72667400-72669200	Active TSS	Rectal Smooth Muscle	rectum
15	chr15:72667400-72669200	Active TSS	GM12878-XiMat	blood
16	chr15:72667400-72669400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:72667400-72669400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:72667400-72669400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr15:72667400-72669400	Active TSS	HepG2	liver
20	chr15:72667600-72669200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:72667600-72669200	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr15:72667600-72669200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr15:72667600-72669200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:72667600-72669200	Active TSS	Esophagus	oesophagus
25	chr15:72667800-72669200	Active TSS	H9 Cell Line	embryonic stem cell
26	chr15:72667800-72669200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:72667800-72669200	Active TSS	Fetal Muscle Trunk	muscle
28	chr15:72667800-72669200	Flanking Active TSS	HMEC	breast
29	chr15:72667800-72669400	Active TSS	Brain Angular Gyrus	brain
30	chr15:72668000-72669200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:72668000-72669200	Active TSS	Right Ventricle	heart
32	chr15:72668200-72669200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr15:72668600-72669200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr15:72668600-72669200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:72668600-72669200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr15:72668600-72669200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:72668600-72669200	Flanking Active TSS	Fetal Muscle Leg	muscle
38	chr15:72668600-72669200	Flanking Active TSS	Placenta	Placenta
39	chr15:72668600-72669200	Active TSS	Right Atrium	heart
40	chr15:72668600-72669200	Flanking Active TSS	NHEK	skin
41	chr15:72668600-72669400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr15:72668600-72669400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr15:72668600-72669400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:72668600-72669400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:72668600-72669400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:72668600-72669400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:72668600-72669400	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr15:72668600-72669400	Flanking Active TSS	Liver	Liver
49	chr15:72668600-72669400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr15:72668600-72669400	Flanking Active TSS	Stomach Smooth Muscle	stomach

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