Variant report

Variant	rs4644832
Chromosome Location	chr15:44084705-44084706
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	YY1	chr15:44084382-44084965	GM12891	blood:	n/a	n/a
2	POLR2A	chr15:44083783-44085630	U87	brain:	n/a	n/a
3	POLR2A	chr15:44083943-44086063	MCF-7	breast:	n/a	n/a
4	MYC	chr15:44084085-44084751	MCF-7	breast:	n/a	chr15:44084416-44084426 chr15:44084286-44084297 chr15:44084225-44084234 chr15:44084416-44084425 chr15:44084415-44084426 chr15:44084417-44084424 chr15:44084287-44084296 chr15:44084224-44084235
5	JUN	chr15:44083241-44086332	K562	blood:	n/a	chr15:44084203-44084216
6	ETS1	chr15:44084454-44084886	K562	blood:	n/a	n/a
7	NFYB	chr15:44084002-44084755	GM12878	blood:	n/a	chr15:44084430-44084444
8	POLR2A	chr15:44084002-44085032	HepG2	liver:	n/a	n/a
9	ELF1	chr15:44084062-44084729	MCF-7	breast:	n/a	n/a
10	TAF1	chr15:44083998-44084763	Hela-S3	cervix:	n/a	n/a
11	MAZ	chr15:44083821-44085064	GM12878	blood:	n/a	chr15:44084416-44084426 chr15:44084920-44084929 chr15:44084286-44084297 chr15:44084225-44084234 chr15:44084416-44084425 chr15:44084415-44084426 chr15:44084417-44084424 chr15:44084287-44084296 chr15:44084224-44084235
12	HMGN3	chr15:44083910-44085094	K562	blood:	n/a	n/a
13	POLR2A	chr15:44084046-44086081	HepG2	liver:	n/a	n/a
14	MAZ	chr15:44083857-44085752	K562	blood:	n/a	chr15:44084416-44084426 chr15:44084920-44084929 chr15:44084286-44084297 chr15:44084225-44084234 chr15:44084416-44084425 chr15:44084415-44084426 chr15:44084417-44084424 chr15:44084287-44084296 chr15:44084224-44084235
15	TBP	chr15:44083740-44084942	K562	blood:	n/a	n/a
16	POLR2A	chr15:44084704-44084959	A549	lung:	n/a	n/a
17	RELA	chr15:44083848-44084997	GM15510	blood:	n/a	n/a
18	RUNX3	chr15:44083992-44085703	GM12878	blood:	n/a	n/a
19	CHD2	chr15:44083951-44085100	K562	blood:	n/a	chr15:44084463-44084473
20	KAP1	chr15:44083891-44084727	HEK293	kidney:	n/a	n/a
21	HEY1	chr15:44083865-44086160	K562	blood:	n/a	n/a
22	RCOR1	chr15:44083898-44084969	HepG2	liver:	n/a	n/a
23	UBTF	chr15:44084191-44085660	K562	blood:	n/a	n/a
24	POU2F2	chr15:44083998-44085132	GM12891	blood:	n/a	n/a
25	ZNF143	chr15:44084058-44084765	GM12878	blood:	n/a	n/a
26	IRF1	chr15:44083785-44084818	K562	blood:	n/a	chr15:44084338-44084352 chr15:44084461-44084475 chr15:44084502-44084516
27	RCOR1	chr15:44083946-44084992	GM12878	blood:	n/a	n/a
28	POLR2A	chr15:44084347-44085147	H1-hESC	embryonic stem cell:	n/a	n/a
29	JUND	chr15:44084077-44084772	A549	lung:	n/a	n/a
30	PAX5	chr15:44083901-44084827	GM12878	blood:	n/a	n/a
31	TAF1	chr15:44083960-44084981	K562	blood:	n/a	n/a
32	MAX	chr15:44083843-44085132	HCT-116	colon:	n/a	chr15:44084416-44084426 chr15:44084920-44084929 chr15:44084286-44084297 chr15:44084225-44084234 chr15:44084416-44084425 chr15:44084415-44084426 chr15:44084417-44084424 chr15:44084287-44084296 chr15:44084224-44084235
33	POLR2A	chr15:44083834-44085206	PANC-1	pancreas:	n/a	n/a
34	POLR2A	chr15:44083801-44085499	HUVEC	blood vessel:	n/a	n/a
35	USF1	chr15:44083736-44084904	ECC-1	luminal epithelium:	n/a	chr15:44084224-44084233 chr15:44084225-44084234 chr15:44084223-44084234 chr15:44084225-44084234 chr15:44084223-44084236 chr15:44084286-44084297
36	STAT1	chr15:44084066-44085109	GM12878	blood:	n/a	chr15:44085013-44085025
37	POLR2A	chr15:44083584-44094591	H1-hESC	embryonic stem cell:	n/a	n/a
38	MXI1	chr15:44083958-44085490	Hela-S3	cervix:	n/a	chr15:44084288-44084297
39	ZKSCAN1	chr15:44084063-44084962	Hela-S3	cervix:	n/a	n/a
40	EGR1	chr15:44084086-44084881	GM12878	blood:	n/a	n/a
41	YY1	chr15:44084284-44084776	SK-N-SH_RA	brain:	n/a	n/a
42	POLR2A	chr15:44083874-44085605	K562	blood:	n/a	n/a
43	POLR2A	chr15:44083906-44084893	K562	blood:	n/a	n/a
44	POLR2A	chr15:44083830-44086157	GM12892	blood:	n/a	n/a
45	POLR2A	chr15:44084403-44084761	A549	lung:	n/a	n/a
46	MAX	chr15:44084042-44084948	HepG2	liver:	n/a	chr15:44084416-44084426 chr15:44084920-44084929 chr15:44084286-44084297 chr15:44084225-44084234 chr15:44084416-44084425 chr15:44084415-44084426 chr15:44084417-44084424 chr15:44084287-44084296 chr15:44084224-44084235
47	MTA3	chr15:44084461-44084880	GM12878	blood:	n/a	n/a
48	CHD2	chr15:44083891-44085083	Hela-S3	cervix:	n/a	chr15:44084463-44084473
49	PAX5	chr15:44084424-44084719	GM12878	blood:	n/a	n/a
50	HCFC1	chr15:44083856-44084781	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:69454228..69455895-chr15:44084318..44086829,2	MCF-7	breast:
2	chr15:43801353..43803228-chr15:44084383..44086214,2	K562	blood:
3	chr15:44082965..44094882-chr15:44108427..44121402,26	K562	blood:
4	chr1:205600117..205601097-chr15:44084113..44084803,2	Hela-S3	cervix:
5	15:44001645-44015047..15:44080886-44089111	Hela-S3	cervix:
6	chr15:44065408..44074556-chr15:44080543..44088380,28	MCF-7	breast:
7	chr15:44084103..44084915-chr3:167451837..167452530,2	Hela-S3	cervix:
8	chr15:44084317..44085015-chr6:13615250..13615759,2	Hela-S3	cervix:
9	chr15:44083909..44084801-chr5:94416865..94417602,2	Hela-S3	cervix:
10	chr15:43800445..43802853-chr15:44084383..44085884,2	K562	blood:
11	chr15:44084564..44085119-chr15:65588109..65588790,2	Hela-S3	cervix:
12	chr15:44084151..44085092-chr20:60961641..60962278,2	Hela-S3	cervix:
13	chr15:44081892..44088686-chr15:44115665..44120334,7	MCF-7	breast:
14	chr15:44084475..44084995-chr19:8454744..8455583,2	NB4	blood:
15	chr10:70091550..70092241-chr15:44084075..44084715,2	NB4	blood:
16	chr15:44084166..44084992-chr16:70834555..70835194,2	Hela-S3	cervix:
17	chr15:44084479..44085334-chr3:31574111..31574813,2	Hela-S3	cervix:
18	chr15:44084024..44084780-chr17:3599023..3599549,2	Hela-S3	cervix:
19	chr15:44084159..44084997-chr9:36190475..36191386,3	Hela-S3	cervix:
20	chr15:44066200..44071612-chr15:44082403..44086035,7	K562	blood:
21	chr12:13153130..13154067-chr15:44084556..44085064,2	Hela-S3	cervix:
22	chr15:44084232..44084939-chr20:30194757..30195707,2	Hela-S3	cervix:
23	chr11:3692345..3692867-chr15:44084030..44084743,2	NB4	blood:
24	chr15:44084225..44084938-chr5:179049834..179050786,2	Hela-S3	cervix:
25	chr15:44082407..44088245-chr15:44114276..44118984,12	MCF-7	breast:
26	chr15:44065227..44073214-chr15:44081584..44094479,46	MCF-7	breast:
27	chr15:44084544..44085334-chr19:572284..572879,2	Hela-S3	cervix:
28	chr1:93644918..93645777-chr15:44084467..44085081,2	Hela-S3	cervix:

Variant related genes	Relation type
SERF2	TF binding region
HYPK	TF binding region
ENSG00000264395	Chromatin interaction
ENSG00000225921	Chromatin interaction
ENSG00000172270	Chromatin interaction
ENSG00000261071	Chromatin interaction
ENSG00000122705	Chromatin interaction
ENSG00000096746	Chromatin interaction
ENSG00000185236	Chromatin interaction
ENSG00000175471	Chromatin interaction
ENSG00000171858	Chromatin interaction
ENSG00000238494	Chromatin interaction
ENSG00000166763	Chromatin interaction
ENSG00000083454	Chromatin interaction
ENSG00000129749	Chromatin interaction
ENSG00000158711	Chromatin interaction
ENSG00000269386	Chromatin interaction
ENSG00000013583	Chromatin interaction
ENSG00000128886	Chromatin interaction
ENSG00000122483	Chromatin interaction
ENSG00000103043	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000163527	Chromatin interaction
ENSG00000114209	Chromatin interaction
ENSG00000166963	Chromatin interaction
ENSG00000140264	Chromatin interaction
ENSG00000140259	Chromatin interaction
ENSG00000110092	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000067369	Chromatin interaction
ENSG00000257950	Chromatin interaction
ENSG00000255621	Chromatin interaction
ENSG00000242866	Chromatin interaction
ENSG00000092470	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10163069	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11070411	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12443084	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17727853	1.00[CEU][hapmap]
rs17795279	1.00[CEU][hapmap]
rs2412821	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2729494	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[EUR][1000 genomes]
rs28410121	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2918943	0.96[YRI][hapmap]
rs2918947	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2930529	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2930530	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2930531	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3102448	0.90[EUR][1000 genomes]
rs3110081	0.83[EUR][1000 genomes]
rs35822148	0.89[EUR][1000 genomes]
rs3862143	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3986209	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4923964	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4923965	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs495880	0.94[CEU][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs514311	0.95[CEU][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs528764	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[EUR][1000 genomes]
rs541871	0.95[CEU][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs62018940	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62018944	0.86[EUR][1000 genomes]
rs6493090	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs654276	0.94[CEU][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs678084	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7174260	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7178230	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8030536	1.00[CEU][hapmap]
rs8038068	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
9	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
10	nsv1036318	chr15:44053617-44160773	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4644832	ZSCAN29	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44083600-44085000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr15:44083600-44085200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:44083600-44085200	Active TSS	Adipose Nuclei	Adipose
4	chr15:44083800-44085000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:44083800-44085200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr15:44083800-44085200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:44083800-44085200	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr15:44083800-44085200	Active TSS	Fetal Brain Female	brain
9	chr15:44083800-44085200	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr15:44083800-44085400	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr15:44083800-44085400	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr15:44083800-44085400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:44083800-44085400	Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr15:44083800-44085400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:44083800-44085400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr15:44083800-44085400	Active TSS	Liver	Liver
17	chr15:44083800-44085400	Active TSS	Brain Angular Gyrus	brain
18	chr15:44083800-44085400	Active TSS	Brain Anterior Caudate	brain
19	chr15:44083800-44085400	Active TSS	Brain Cingulate Gyrus	brain
20	chr15:44083800-44085400	Active TSS	Brain Hippocampus Middle	brain
21	chr15:44083800-44085400	Active TSS	Brain Substantia Nigra	brain
22	chr15:44083800-44085400	Active TSS	Colonic Mucosa	Colon
23	chr15:44083800-44085400	Active TSS	Colon Smooth Muscle	Colon
24	chr15:44083800-44085400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr15:44083800-44085400	Active TSS	Fetal Lung	lung
26	chr15:44083800-44085400	Active TSS	Fetal Muscle Trunk	muscle
27	chr15:44083800-44085400	Active TSS	Thymus	Thymus
28	chr15:44083800-44085600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:44083800-44085600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr15:44083800-44085600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:44083800-44085600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:44083800-44085600	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr15:44083800-44085600	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr15:44083800-44085600	Active TSS	Esophagus	oesophagus
35	chr15:44083800-44085600	Active TSS	Fetal Kidney	kidney
36	chr15:44083800-44085600	Active TSS	Left Ventricle	heart
37	chr15:44083800-44085600	Active TSS	Ovary	ovary
38	chr15:44083800-44085600	Active TSS	Right Ventricle	heart
39	chr15:44083800-44085600	Active TSS	NHLF	lung
40	chr15:44083800-44085800	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr15:44083800-44085800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:44083800-44085800	Active TSS	Aorta	Aorta
43	chr15:44083800-44085800	Active TSS	Right Atrium	heart
44	chr15:44083800-44086000	Active TSS	A549	lung
45	chr15:44083800-44086800	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr15:44084000-44084800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:44084000-44085000	Active TSS	Primary B cells from cord blood	blood
48	chr15:44084000-44085000	Active TSS	Primary hematopoietic stem cells	blood
49	chr15:44084000-44085200	Active TSS	Duodenum Mucosa	Duodenum
50	chr15:44084000-44085400	Active TSS	H1 Cell Line	embryonic stem cell

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