Variant report

Variant	rs16945097
Chromosome Location	chr15:45880122-45880123
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	EP300	chr15:45878650-45880212	GM12878	blood:	n/a	chr15:45879834-45879850 chr15:45878679-45878693 chr15:45879872-45879881 chr15:45879827-45879843 chr15:45879833-45879849 chr15:45879161-45879174 chr15:45879528-45879535
2	POLR2A	chr15:45878163-45880140	K562	blood:	n/a	n/a
3	POLR2A	chr15:45878805-45880174	H1-hESC	embryonic stem cell:	n/a	n/a
4	GABPA	chr15:45878784-45880396	MCF-7	breast:	n/a	n/a
5	POLR2A	chr15:45878113-45881140	HepG2	liver:	n/a	n/a
6	GABPA	chr15:45878964-45880234	HL-60	blood:	n/a	n/a
7	MYBL2	chr15:45879004-45880128	HepG2	liver:	n/a	n/a
8	MAFK	chr15:45879260-45880206	HepG2	liver:	n/a	chr15:45879401-45879417 chr15:45879398-45879413
9	STAT3	chr15:45879373-45880299	MCF10A-Er-Src	breast:	n/a	chr15:45880038-45880049
10	BCLAF1	chr15:45879042-45880237	GM12878	blood:	n/a	chr15:45879829-45879842 chr15:45879527-45879536 chr15:45879558-45879571
11	POLR2A	chr15:45879022-45880293	HCT-116	colon:	n/a	n/a
12	MAFK	chr15:45879252-45880734	IMR90	lung:	n/a	chr15:45880420-45880431 chr15:45879401-45879417 chr15:45880420-45880431 chr15:45880419-45880430 chr15:45880419-45880430 chr15:45879398-45879413
13	GABPA	chr15:45878777-45880182	A549	lung:	n/a	n/a
14	MAX	chr15:45878985-45880169	HCT-116	colon:	n/a	n/a
15	MAFF	chr15:45879078-45880259	HepG2	liver:	n/a	n/a
16	MXI1	chr15:45879018-45880478	GM12878	blood:	n/a	n/a
17	STAT1	chr15:45878948-45880142	GM12878	blood:	n/a	n/a
18	NFYA	chr15:45879182-45880372	Hela-S3	cervix:	n/a	chr15:45879366-45879384 chr15:45879999-45880009
19	ELK1	chr15:45878979-45880352	GM12878	blood:	n/a	n/a
20	ATF2	chr15:45878999-45880286	GM12878	blood:	n/a	chr15:45880074-45880085
21	POLR2A	chr15:45878631-45880225	Hela-S3	cervix:	n/a	n/a
22	TBP	chr15:45878915-45880202	H1-hESC	embryonic stem cell:	n/a	n/a
23	HCFC1	chr15:45878355-45881226	Hela-S3	cervix:	n/a	n/a
24	CUX1	chr15:45879209-45880131	GM12878	blood:	n/a	n/a
25	EP300	chr15:45878778-45880124	K562	blood:	n/a	chr15:45879834-45879850 chr15:45879872-45879881 chr15:45879827-45879843 chr15:45879833-45879849 chr15:45879161-45879174 chr15:45879528-45879535
26	POLR2A	chr15:45879092-45880147	HCT-116	colon:	n/a	n/a
27	ZKSCAN1	chr15:45879201-45880382	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr15:45878113-45880658	MCF10A-Er-Src	breast:	n/a	n/a
29	MXI1	chr15:45878135-45881322	SK-N-SH	brain:	n/a	n/a
30	SIN3AK20	chr15:45879200-45880186	PANC-1	pancreas:	n/a	n/a
31	MAZ	chr15:45879059-45880152	Hela-S3	cervix:	n/a	n/a
32	MTA3	chr15:45879792-45880400	GM12878	blood:	n/a	n/a
33	MAX	chr15:45878998-45880153	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr15:45878919-45880161	U87	brain:	n/a	n/a
35	CHD2	chr15:45879001-45880251	GM12878	blood:	n/a	chr15:45879275-45879285
36	ATF1	chr15:45879114-45880171	K562	blood:	n/a	n/a
37	POLR2A	chr15:45879156-45880155	GM10847	blood:	n/a	n/a
38	POLR2A	chr15:45878045-45880372	GM12878	blood:	n/a	n/a
39	TBP	chr15:45879080-45880123	K562	blood:	n/a	n/a
40	E2F4	chr15:45879377-45880318	MCF10A-Er-Src	breast:	n/a	chr15:45879872-45879881 chr15:45879823-45879830
41	ATF2	chr15:45879780-45880143	H1-hESC	embryonic stem cell:	n/a	chr15:45880074-45880085
42	TAF1	chr15:45878507-45880319	H1-neurons	neurons:	n/a	n/a
43	RELA	chr15:45879137-45880169	GM18951	blood:	n/a	n/a
44	RELA	chr15:45878860-45880342	GM15510	blood:	n/a	n/a
45	POLR2A	chr15:45879078-45880156	HepG2	liver:	n/a	n/a
46	PML	chr15:45878911-45880169	K562	blood:	n/a	n/a
47	REST	chr15:45878015-45880689	H1-neurons	neurons:	n/a	chr15:45879843-45879863
48	JUND	chr15:45879921-45880267	HepG2	liver:	n/a	n/a
49	SMC3	chr15:45879081-45880290	Hela-S3	cervix:	n/a	n/a
50	UBTF	chr15:45879082-45880320	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:45749728..45751620-chr15:45879079..45880705,2	MCF-7	breast:
2	chr15:45694563..45696942-chr15:45878361..45881039,2	K562	blood:
3	chr15:45813492..45816353-chr15:45876550..45880712,4	MCF-7	breast:
4	chr15:45879453..45880229-chr16:74734570..74735389,2	Hela-S3	cervix:
5	chr15:45855963..45859182-chr15:45877803..45880512,3	MCF-7	breast:
6	chr15:45750236..45753171-chr15:45878645..45880450,2	MCF-7	breast:
7	chr15:45490877..45493855-chr15:45879081..45881062,2	K562	blood:
8	chr15:45877908..45881944-chr15:45926466..45928753,3	MCF-7	breast:
9	chr15:45694198..45696265-chr15:45878361..45881505,3	K562	blood:
10	chr15:45693513..45696404-chr15:45876472..45881031,4	MCF-7	breast:
11	chr15:45878966..45881006-chr15:45882996..45885480,3	MCF-7	breast:
12	chr15:45740795..45743926-chr15:45878461..45880935,3	MCF-7	breast:
13	chr15:45693316..45695933-chr15:45878534..45881095,2	MCF-7	breast:
14	chr15:45749404..45751481-chr15:45878948..45881186,2	K562	blood:
15	chr15:45875078..45876854-chr15:45880097..45881754,2	MCF-7	breast:
16	chr15:45813395..45816326-chr15:45879088..45881474,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200419	TF binding region
BLOC1S6	TF binding region
ENSG00000179362	Chromatin interaction
ENSG00000259932	Chromatin interaction
ENSG00000260035	Chromatin interaction
ENSG00000259354	Chromatin interaction
ENSG00000200419	Chromatin interaction
ENSG00000171763	Chromatin interaction
ENSG00000168404	Chromatin interaction
ENSG00000138606	Chromatin interaction
ENSG00000137767	Chromatin interaction
ENSG00000171766	Chromatin interaction
ENSG00000259427	Chromatin interaction
ENSG00000104164	Chromatin interaction
ENSG00000104154	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11632553	0.83[CEU][hapmap]
rs11637984	0.83[CEU][hapmap]
rs16946621	0.87[CEU][hapmap]
rs17627219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1966763	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2083728	1.00[CEU][hapmap]
rs55755923	0.91[EUR][1000 genomes]
rs55806911	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55913172	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55997350	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56081351	0.92[EUR][1000 genomes]
rs56179992	0.84[ASN][1000 genomes]
rs56190351	0.92[EUR][1000 genomes]
rs56259807	0.92[EUR][1000 genomes]
rs56304405	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56375332	0.92[EUR][1000 genomes]
rs56395216	0.92[EUR][1000 genomes]
rs57291883	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59593563	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60351453	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60378269	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60992352	0.84[ASN][1000 genomes]
rs61209164	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68044128	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs685812	1.00[CEU][hapmap]
rs7164956	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7165827	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7169748	1.00[JPT][hapmap]
rs7170090	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7175288	0.94[CEU][hapmap]
rs7178395	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7178879	1.00[ASN][1000 genomes]
rs7179265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179903	1.00[ASN][1000 genomes]
rs7181436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72711301	0.84[ASN][1000 genomes]
rs72713103	0.84[ASN][1000 genomes]
rs72713104	0.84[ASN][1000 genomes]
rs72713105	0.84[ASN][1000 genomes]
rs72713106	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713107	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713168	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713169	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713171	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713172	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713175	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713177	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72713178	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72713180	0.81[EUR][1000 genomes]
rs72713182	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72713185	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72713191	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72713197	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72713199	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72713201	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72715003	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72715005	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72715008	0.91[EUR][1000 genomes]
rs72715010	0.92[EUR][1000 genomes]
rs72715014	0.92[EUR][1000 genomes]
rs72715019	0.92[EUR][1000 genomes]
rs72715020	0.92[EUR][1000 genomes]
rs72715077	0.92[EUR][1000 genomes]
rs8025407	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs8039784	0.83[CEU][hapmap]
rs8041902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043334	1.00[CEU][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045556	chr15:45777396-45884854	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv904188	chr15:45801035-45941689	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16945097	SLC30A4	cis	parietal	SCAN
rs16945097	GPR176	cis	cerebellum	SCAN
rs16945097	MGA	cis	parietal	SCAN
rs16945097	RPAP1	cis	cerebellum	SCAN
rs16945097	TMEM62	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45877400-45881800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:45878000-45880800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr15:45878200-45880600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr15:45878200-45880800	Active TSS	H1 Cell Line	embryonic stem cell
5	chr15:45878200-45880800	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr15:45878200-45880800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:45878400-45880400	Active TSS	Fetal Intestine Small	intestine
8	chr15:45878400-45880600	Active TSS	HSMMtube	muscle
9	chr15:45878400-45881000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr15:45878400-45881000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:45878400-45881200	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr15:45878600-45880400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:45878600-45880400	Active TSS	A549	lung
14	chr15:45878600-45880400	Bivalent/Poised TSS	HepG2	liver
15	chr15:45878600-45880600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:45878600-45880600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:45878600-45880600	Active TSS	Left Ventricle	heart
18	chr15:45878600-45880800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:45878600-45880800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:45878600-45880800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:45878600-45880800	Active TSS	Ovary	ovary
22	chr15:45878600-45880800	Active TSS	K562	blood
23	chr15:45878600-45881000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:45878600-45881000	Active TSS	Fetal Muscle Trunk	muscle
25	chr15:45878600-45881800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:45878800-45880200	Active TSS	Fetal Lung	lung
27	chr15:45878800-45880200	Active TSS	Rectal Smooth Muscle	rectum
28	chr15:45878800-45880200	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr15:45878800-45880200	Active TSS	Thymus	Thymus
30	chr15:45878800-45880400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr15:45878800-45880400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr15:45878800-45880400	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr15:45878800-45880400	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr15:45878800-45880400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr15:45878800-45880400	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr15:45878800-45880400	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr15:45878800-45880400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:45878800-45880400	Active TSS	Gastric	stomach
39	chr15:45878800-45880400	Active TSS	Lung	lung
40	chr15:45878800-45880400	Active TSS	Stomach Mucosa	stomach
41	chr15:45878800-45880600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr15:45878800-45880600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:45878800-45880600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:45878800-45880600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:45878800-45880600	Active TSS	Brain Hippocampus Middle	brain
46	chr15:45878800-45880600	Active TSS	Colon Smooth Muscle	Colon
47	chr15:45878800-45880600	Active TSS	Fetal Brain Male	brain
48	chr15:45878800-45880600	Active TSS	Fetal Stomach	stomach
49	chr15:45878800-45880600	Active TSS	Fetal Thymus	thymus
50	chr15:45878800-45880600	Active TSS	Pancreas	Pancrea

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