Variant report

Variant	rs56066141
Chromosome Location	chr15:75069974-75069975
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	POU2F2	chr15:75069653-75070099	GM12878	blood:	n/a	n/a
2	EBF1	chr15:75069053-75070594	GM12878	blood:	n/a	chr15:75070178-75070187 chr15:75070176-75070189 chr15:75069993-75070003 chr15:75070177-75070187 chr15:75069991-75070004 chr15:75069992-75070003 chr15:75069355-75069365 chr15:75069993-75070002
3	RELA	chr15:75069497-75070566	GM18505	blood:	n/a	n/a
4	NFATC1	chr15:75069483-75070105	GM12878	blood:	n/a	n/a
5	EP300	chr15:75069684-75070267	GM12878	blood:	n/a	chr15:75069712-75069728
6	EP300	chr15:75069720-75069987	GM12878	blood:	n/a	n/a
7	TBL1XR1	chr15:75069234-75070185	GM12878	blood:	n/a	n/a
8	CEBPB	chr15:75069276-75070271	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:75069024-75070576	HL-60	blood:	n/a	n/a
10	MAZ	chr15:75069358-75070539	GM12878	blood:	n/a	n/a
11	ETS1	chr15:75069511-75070087	GM12878	blood:	n/a	chr15:75069571-75069580
12	POLR2A	chr15:75069250-75070730	Raji	blood:	n/a	n/a
13	POLR2A	chr15:75069164-75069982	GM12891	blood:	n/a	n/a
14	BCLAF1	chr15:75069034-75070213	GM12878	blood:	n/a	chr15:75069691-75069699
15	NFATC1	chr15:75069433-75070146	GM12878	blood:	n/a	n/a
16	BCL11A	chr15:75069736-75070056	GM12878	blood:	n/a	n/a
17	TCF3	chr15:75069550-75070008	GM12878	blood:	n/a	chr15:75069792-75069801 chr15:75069789-75069804
18	POLR2A	chr15:75069206-75070548	GM18505	blood:	n/a	n/a
19	POLR2A	chr15:75069101-75070634	GM12891	blood:	n/a	n/a
20	POLR2A	chr15:75069268-75070153	GM12891	blood:	n/a	n/a
21	SP1	chr15:75069624-75070098	GM12878	blood:	n/a	n/a
22	ELF1	chr15:75069659-75069988	K562	blood:	n/a	chr15:75069848-75069861
23	RUNX3	chr15:75069087-75070686	GM12878	blood:	n/a	n/a
24	NFIC	chr15:75069493-75070170	GM12878	blood:	n/a	chr15:75069756-75069784
25	MXI1	chr15:75069172-75070185	GM12878	blood:	n/a	n/a
26	MAX	chr15:75069570-75070583	GM12878	blood:	n/a	n/a
27	POLR2A	chr15:75069443-75070573	GM18951	blood:	n/a	n/a
28	ELF1	chr15:75069013-75070158	GM12878	blood:	n/a	chr15:75069848-75069861
29	SMC3	chr15:75069706-75070454	GM12878	blood:	n/a	n/a
30	POLR2A	chr15:75069268-75070336	GM12891	blood:	n/a	n/a
31	POLR2A	chr15:75069466-75070011	GM12892	blood:	n/a	n/a
32	WRNIP1	chr15:75069246-75070403	GM12878	blood:	n/a	n/a
33	MYC	chr15:75069416-75070153	NB4	blood:	n/a	n/a
34	STAT5A	chr15:75068873-75070340	GM12878	blood:	n/a	chr15:75069984-75069996 chr15:75069144-75069151 chr15:75069202-75069210
35	TCF12	chr15:75069630-75070125	GM12878	blood:	n/a	n/a
36	EBF1	chr15:75069070-75070620	GM12878	blood:	n/a	chr15:75070178-75070187 chr15:75070176-75070189 chr15:75069993-75070003 chr15:75070177-75070187 chr15:75069991-75070004 chr15:75069992-75070003 chr15:75069355-75069365 chr15:75069993-75070002
37	POLR2A	chr15:75068864-75070645	GM12892	blood:	n/a	n/a
38	PAX5	chr15:75069685-75070027	GM12878	blood:	n/a	n/a
39	POLR2A	chr15:75069088-75070635	GM12892	blood:	n/a	n/a
40	ZNF143	chr15:75069805-75070146	GM12878	blood:	n/a	chr15:75069985-75070003
41	REST	chr15:75069448-75070062	PFSK-1	brain:	n/a	chr15:75069689-75069698
42	TCF12	chr15:75069646-75070025	GM12878	blood:	n/a	n/a
43	CHD2	chr15:75069412-75070273	GM12878	blood:	n/a	n/a
44	FOXM1	chr15:75069523-75070678	GM12878	blood:	n/a	n/a
45	BHLHE40	chr15:75069572-75070504	GM12878	blood:	n/a	n/a
46	POLR2A	chr15:75068779-75070595	GM12878	blood:	n/a	n/a
47	SPI1	chr15:75069257-75070450	GM12878	blood:	n/a	chr15:75069849-75069862
48	ATF2	chr15:75069574-75070191	GM12878	blood:	n/a	n/a
49	NFIC	chr15:75069026-75070765	GM12878	blood:	n/a	chr15:75069282-75069298 chr15:75069488-75069505 chr15:75069270-75069298 chr15:75069756-75069784
50	CUX1	chr15:75069657-75070447	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75069513..75071369-chr15:75076004..75078063,2	K562	blood:
2	chr15:75069556..75072054-chr15:75126670..75129004,2	MCF-7	breast:
3	chr15:75067632..75072081-chr15:75073195..75075797,6	MCF-7	breast:
4	chr15:74920881..74923139-chr15:75069434..75070977,2	MCF-7	breast:
5	chr15:74923393..74925278-chr15:75068761..75070889,2	MCF-7	breast:

Variant related genes	Relation type
CSK	TF binding region
ENSG00000179335	Chromatin interaction
ENSG00000103653	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11553762	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11631294	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11631682	0.95[ASN][1000 genomes]
rs11631689	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631817	0.87[ASN][1000 genomes]
rs11632547	0.93[ASN][1000 genomes]
rs11632706	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11632814	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11632822	0.95[ASN][1000 genomes]
rs11633539	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11633861	0.90[ASN][1000 genomes]
rs11636256	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637637	0.87[ASN][1000 genomes]
rs16972511	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972853	0.87[ASN][1000 genomes]
rs17861124	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17861125	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17861130	0.87[ASN][1000 genomes]
rs17861138	0.90[ASN][1000 genomes]
rs17861139	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17861141	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17861142	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17861145	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2069519	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2069521	0.93[ASN][1000 genomes]
rs2069522	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2069524	0.90[ASN][1000 genomes]
rs2069525	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2069526	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35197434	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35331038	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35408600	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4646425	0.93[ASN][1000 genomes]
rs4646427	0.93[ASN][1000 genomes]
rs56748048	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59902765	0.87[ASN][1000 genomes]
rs74025837	0.95[ASN][1000 genomes]
rs74025839	0.95[ASN][1000 genomes]
rs74025842	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74025843	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74025847	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75065600-75072600	Enhancers	Primary hematopoietic stem cells	blood
2	chr15:75065600-75073200	Weak transcription	Brain Angular Gyrus	brain
3	chr15:75065600-75073600	Enhancers	Fetal Intestine Large	intestine
4	chr15:75065600-75073600	Enhancers	Fetal Intestine Small	intestine
5	chr15:75065800-75072800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr15:75066200-75073000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:75066400-75072400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr15:75066400-75072800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:75066600-75070000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:75066600-75072600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:75067200-75072800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:75067400-75071000	Enhancers	Brain Hippocampus Middle	brain
13	chr15:75067400-75074200	Enhancers	Stomach Mucosa	stomach
14	chr15:75067600-75070400	Enhancers	Brain Anterior Caudate	brain
15	chr15:75067600-75070400	Enhancers	Brain Cingulate Gyrus	brain
16	chr15:75067600-75071200	Enhancers	Placenta	Placenta
17	chr15:75067600-75071800	Enhancers	Spleen	Spleen
18	chr15:75067600-75071800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr15:75067800-75071800	Enhancers	Small Intestine	intestine
20	chr15:75067800-75072000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr15:75068000-75073200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:75068600-75070800	Enhancers	Fetal Muscle Leg	muscle
23	chr15:75068600-75071000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr15:75068800-75070400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:75068800-75071200	Enhancers	Esophagus	oesophagus
26	chr15:75068800-75071400	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr15:75068800-75073400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr15:75069000-75070000	Enhancers	Fetal Heart	heart
29	chr15:75069000-75070200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:75069000-75070200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:75069000-75070200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:75069000-75070200	Enhancers	Stomach Smooth Muscle	stomach
33	chr15:75069000-75070200	Enhancers	HSMMtube	muscle
34	chr15:75069000-75070400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:75069000-75070400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr15:75069000-75070400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:75069000-75070400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr15:75069000-75070400	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr15:75069000-75070400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr15:75069000-75070400	Enhancers	Right Atrium	heart
41	chr15:75069000-75070600	Enhancers	Brain Substantia Nigra	brain
42	chr15:75069000-75070600	Enhancers	Fetal Stomach	stomach
43	chr15:75069000-75070600	Enhancers	Lung	lung
44	chr15:75069000-75070600	Flanking Active TSS	GM12878-XiMat	blood
45	chr15:75069000-75070600	Flanking Active TSS	HepG2	liver
46	chr15:75069000-75070800	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr15:75069000-75070800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:75069000-75070800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:75069000-75070800	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr15:75069000-75070800	Enhancers	HUVEC	blood vessel

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