Variant report

Variant	rs10467946
Chromosome Location	chr15:72978996-72978997
allele	G/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	FOS	chr15:72978830-72979032	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr15:72977861-72979012	K562	blood:	n/a	n/a
3	POLR2A	chr15:72977747-72978998	HEK293	kidney:	n/a	n/a
4	STAT3	chr15:72978410-72979262	MCF10A-Er-Src	breast:	n/a	chr15:72978963-72978974
5	YY1	chr15:72978238-72979028	SK-N-SH_RA	brain:	n/a	chr15:72978283-72978297 chr15:72978875-72978883 chr15:72978558-72978578
6	TAF1	chr15:72978023-72979015	K562	blood:	n/a	n/a
7	MXI1	chr15:72978070-72979102	HepG2	liver:	n/a	n/a
8	ELF1	chr15:72977877-72979260	MCF-7	breast:	n/a	chr15:72978502-72978511
9	GTF2F1	chr15:72978052-72979012	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIX5	chr15:72978030-72979465	A549	lung:	n/a	n/a
11	MAX	chr15:72978057-72979094	NB4	blood:	n/a	chr15:72978711-72978721
12	CHD1	chr15:72978057-72979015	GM12878	blood:	n/a	n/a
13	HDAC2	chr15:72978147-72979070	MCF-7	breast:	n/a	n/a
14	POLR2A	chr15:72978205-72978999	HepG2	liver:	n/a	n/a
15	ETS1	chr15:72978304-72979014	GM12878	blood:	n/a	chr15:72978533-72978543 chr15:72978535-72978544 chr15:72978535-72978544 chr15:72978534-72978547 chr15:72978501-72978510
16	GABPA	chr15:72977978-72979056	A549	lung:	n/a	chr15:72978711-72978720 chr15:72978504-72978511
17	TAF1	chr15:72977934-72979140	A549	lung:	n/a	n/a
18	MAZ	chr15:72978221-72979039	Hela-S3	cervix:	n/a	chr15:72978711-72978721
19	YY1	chr15:72978111-72979047	ECC-1	luminal epithelium:	n/a	chr15:72978283-72978297 chr15:72978875-72978883 chr15:72978558-72978578
20	TCF7L2	chr15:72978191-72979056	Hela-S3	cervix:	n/a	n/a
21	YY1	chr15:72978117-72979057	K562	blood:	n/a	chr15:72978283-72978297 chr15:72978875-72978883 chr15:72978558-72978578
22	REST	chr15:72977704-72979414	H1-neurons	neurons:	n/a	chr15:72977715-72977725
23	WRNIP1	chr15:72978028-72979111	GM12878	blood:	n/a	n/a
24	POLR2A	chr15:72977891-72979174	SK-N-MC	brain:	n/a	n/a
25	GATA2	chr15:72977994-72979227	SH-SY5Y	brain:	n/a	chr15:72978214-72978227 chr15:72978097-72978113 chr15:72978100-72978109
26	MAZ	chr15:72977987-72979034	GM12878	blood:	n/a	chr15:72978711-72978721
27	SIN3AK20	chr15:72977647-72979500	MCF-7	breast:	n/a	n/a
28	EP300	chr15:72978100-72979095	GM12878	blood:	n/a	chr15:72978540-72978556 chr15:72978536-72978543
29	MAX	chr15:72977990-72979175	A549	lung:	n/a	chr15:72978711-72978721
30	RCOR1	chr15:72978224-72979280	Hela-S3	cervix:	n/a	n/a
31	FOXA1	chr15:72978962-72979329	T-47D	breast:	n/a	n/a
32	BHLHE40	chr15:72978207-72979046	K562	blood:	n/a	n/a
33	POLR2A	chr15:72977937-72979067	HUVEC	blood vessel:	n/a	n/a
34	GABPA	chr15:72977917-72979053	A549	lung:	n/a	chr15:72978711-72978720 chr15:72978504-72978511
35	POLR2A	chr15:72977988-72979179	Hela-S3	cervix:	n/a	n/a
36	MXI1	chr15:72977425-72979188	IMR90	lung:	n/a	n/a
37	RELA	chr15:72978217-72979112	GM18951	blood:	n/a	n/a
38	CHD2	chr15:72978125-72979142	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr15:72977895-72979033	Raji	blood:	n/a	n/a
40	POLR2A	chr15:72978192-72979025	Gliobla	brain:	n/a	n/a
41	YY1	chr15:72978171-72979189	SK-N-SH	brain:	n/a	chr15:72978283-72978297 chr15:72978875-72978883 chr15:72978558-72978578
42	BCL3	chr15:72978144-72979170	A549	lung:	n/a	chr15:72978619-72978632
43	GATA3	chr15:72977958-72979410	A549	lung:	n/a	chr15:72978214-72978227 chr15:72978097-72978113 chr15:72978100-72978109
44	REST	chr15:72978229-72979024	A549	lung:	n/a	n/a
45	POLR2A	chr15:72978059-72979002	GM12878	blood:	n/a	n/a
46	RCOR1	chr15:72978047-72979239	K562	blood:	n/a	n/a
47	POLR2A	chr15:72978039-72979092	PANC-1	pancreas:	n/a	n/a
48	MAX	chr15:72978226-72979039	Hela-S3	cervix:	n/a	chr15:72978711-72978721
49	ELK4	chr15:72978082-72979267	Hela-S3	cervix:	n/a	chr15:72978499-72978510
50	CTCF	chr15:72978960-72979110	GM12868	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:72978938..72981317-chr15:73074560..73077463,3	K562	blood:
2	chr15:72971779..72975423-chr15:72976170..72980827,7	K562	blood:
3	chr10:112257437..112258408-chr15:72978244..72979060,2	Hela-S3	cervix:
4	chr15:72978405..72979084-chr15:73076020..73076684,2	Hela-S3	cervix:
5	chr15:72521683..72524680-chr15:72976957..72979803,2	K562	blood:
6	chr15:72973101..72975344-chr15:72976692..72980792,4	MCF-7	breast:
7	chr15:72562851..72564645-chr15:72977653..72979663,2	K562	blood:
8	chr15:72521996..72524543-chr15:72977386..72979463,3	MCF-7	breast:
9	chr12:112846958..112847755-chr15:72978300..72979259,2	Hela-S3	cervix:
10	chr15:72978938..72981317-chr15:73074560..73077463,2	K562	blood:
11	chr15:72978281..72979189-chr16:89119223..89119876,2	NB4	blood:
12	chr15:72978250..72978999-chr17:62502049..62502770,2	NB4	blood:
13	chr15:72978470..72980550-chr15:73014196..73015991,2	K562	blood:
14	chr15:72764850..72767674-chr15:72977020..72979928,5	K562	blood:

Variant related genes	Relation type
ENSG00000261281	TF binding region
HIGD2B	TF binding region
BBS4	TF binding region
ENSG00000067225	Chromatin interaction
ENSG00000140463	Chromatin interaction
ENSG00000258890	Chromatin interaction
ENSG00000261281	Chromatin interaction
ENSG00000137817	Chromatin interaction
ENSG00000260898	Chromatin interaction
ENSG00000138166	Chromatin interaction
ENSG00000159322	Chromatin interaction
ENSG00000089009	Chromatin interaction
ENSG00000166233	Chromatin interaction
ENSG00000256982	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000261423	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11858132	1.00[ASN][1000 genomes]
rs12917453	1.00[JPT][hapmap]
rs13379630	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2277597	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35731345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816151	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57287802	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57551071	0.93[ASN][1000 genomes]
rs57769940	1.00[EUR][1000 genomes]
rs58429461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59686861	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60154507	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758386	chr15:72819785-73120560	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv2760039	chr15:72819785-73120560	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv428307	chr15:72819785-73120560	Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	esv3430383	chr15:72821093-73035167	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72977400-72979400	Active TSS	GM12878-XiMat	blood
2	chr15:72977400-72979600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:72977400-72979600	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr15:72977400-72979800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:72977400-72980000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:72977400-72980200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr15:72977600-72979400	Active TSS	H1 Cell Line	embryonic stem cell
8	chr15:72977600-72979400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr15:72977600-72979400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr15:72977600-72979600	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr15:72977600-72979600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:72977600-72979800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:72977600-72979800	Active TSS	Fetal Intestine Large	intestine
14	chr15:72977600-72979800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr15:72977600-72979800	Active TSS	Thymus	Thymus
16	chr15:72977800-72979000	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr15:72977800-72979200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:72977800-72979200	Active TSS	Esophagus	oesophagus
19	chr15:72977800-72979200	Active TSS	Gastric	stomach
20	chr15:72977800-72979200	Active TSS	Pancreas	Pancrea
21	chr15:72977800-72979200	Active TSS	Small Intestine	intestine
22	chr15:72977800-72979400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:72977800-72979400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr15:72977800-72979400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:72977800-72979400	Active TSS	Brain Anterior Caudate	brain
26	chr15:72977800-72979400	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr15:72977800-72979400	Active TSS	Brain Substantia Nigra	brain
28	chr15:72977800-72979400	Active TSS	Fetal Muscle Trunk	muscle
29	chr15:72977800-72979400	Active TSS	Stomach Mucosa	stomach
30	chr15:72977800-72979600	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr15:72977800-72979600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:72977800-72979600	Active TSS	Fetal Kidney	kidney
33	chr15:72977800-72979600	Active TSS	Psoas Muscle	Psoas
34	chr15:72977800-72979600	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr15:72977800-72979600	Active TSS	HMEC	breast
36	chr15:72977800-72979800	Active TSS	Fetal Intestine Small	intestine
37	chr15:72977800-72980000	Active TSS	Colonic Mucosa	Colon
38	chr15:72978000-72979000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr15:72978000-72979000	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr15:72978000-72979000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr15:72978000-72979000	Active TSS	Brain Cingulate Gyrus	brain
42	chr15:72978000-72979000	Active TSS	Duodenum Mucosa	Duodenum
43	chr15:72978000-72979000	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr15:72978000-72979200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:72978000-72979200	Active TSS	Lung	lung
46	chr15:72978000-72979200	Active TSS	Spleen	Spleen
47	chr15:72978000-72979400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr15:72978000-72979400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr15:72978000-72979400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:72978000-72979400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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