Variant report

Variant	rs954144
Chromosome Location	chr15:78730591-78730592
allele	A/C/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	GABPA	chr15:78730041-78730851	MCF-7	breast:	n/a	n/a
2	POLR2A	chr15:78729851-78730917	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr15:78729743-78730747	K562	blood:	n/a	chr15:78730383-78730399
4	SIN3AK20	chr15:78729604-78731522	MCF-7	breast:	n/a	n/a
5	TCF7L2	chr15:78730171-78731550	HCT-116	colon:	n/a	n/a
6	MXI1	chr15:78729797-78731602	HepG2	liver:	n/a	n/a
7	POLR2A	chr15:78729768-78730831	GM12891	blood:	n/a	n/a
8	TAF1	chr15:78729742-78731273	A549	lung:	n/a	n/a
9	FOXA1	chr15:78730162-78730699	HepG2	liver:	n/a	n/a
10	BCL3	chr15:78729858-78730622	A549	lung:	n/a	chr15:78730387-78730396 chr15:78730444-78730453
11	SRF	chr15:78729785-78730947	MCF-7	breast:	n/a	chr15:78730122-78730132
12	MAZ	chr15:78729948-78731452	GM12878	blood:	n/a	chr15:78730153-78730162 chr15:78731240-78731250
13	TAF1	chr15:78729730-78731552	K562	blood:	n/a	n/a
14	POLR2A	chr15:78729509-78731589	HL-60	blood:	n/a	n/a
15	ZNF263	chr15:78730393-78731149	K562	blood:	n/a	chr15:78730598-78730607
16	POU2F2	chr15:78729763-78730878	GM12878	blood:	n/a	n/a
17	FOSL2	chr15:78729916-78730831	A549	lung:	n/a	n/a
18	TAF1	chr15:78729757-78730867	PFSK-1	brain:	n/a	n/a
19	PAX5	chr15:78729918-78730692	GM12878	blood:	n/a	n/a
20	TCF12	chr15:78729518-78731361	A549	lung:	n/a	n/a
21	FOXA1	chr15:78730212-78730594	T-47D	breast:	n/a	n/a
22	ZBTB33	chr15:78730177-78730652	HepG2	liver:	n/a	chr15:78730541-78730550 chr15:78730396-78730411 chr15:78730399-78730409 chr15:78730413-78730428
23	SPI1	chr15:78730311-78730673	GM12891	blood:	n/a	chr15:78730445-78730458
24	MYC	chr15:78729717-78730640	K562	blood:	n/a	chr15:78730153-78730162
25	TAF1	chr15:78729923-78731018	ECC-1	luminal epithelium:	n/a	n/a
26	BCL3	chr15:78729706-78730857	A549	lung:	n/a	chr15:78730387-78730396 chr15:78730444-78730453 chr15:78730637-78730650
27	TAF1	chr15:78730073-78730878	MCF-7	breast:	n/a	n/a
28	JUND	chr15:78729777-78731496	K562	blood:	n/a	chr15:78731045-78731054 chr15:78731288-78731300
29	FOXM1	chr15:78729981-78730758	GM12878	blood:	n/a	n/a
30	SP1	chr15:78730077-78730619	HepG2	liver:	n/a	chr15:78730387-78730396 chr15:78730444-78730453 chr15:78730443-78730455 chr15:78730388-78730397 chr15:78730386-78730397 chr15:78730443-78730455 chr15:78730386-78730398 chr15:78730444-78730458 chr15:78730386-78730398
31	HEY1	chr15:78729897-78731727	HepG2	liver:	n/a	chr15:78730387-78730402
32	UBTF	chr15:78730423-78731578	K562	blood:	n/a	n/a
33	ZBTB33	chr15:78730010-78731058	HepG2	liver:	n/a	chr15:78730541-78730550 chr15:78730396-78730411 chr15:78730399-78730409 chr15:78730413-78730428
34	MAX	chr15:78729885-78730789	H1-hESC	embryonic stem cell:	n/a	chr15:78730153-78730162
35	MYC	chr15:78729895-78730750	MCF-7	breast:	n/a	chr15:78730153-78730162
36	POLR2A	chr15:78729551-78731141	NB4	blood:	n/a	n/a
37	POLR2A	chr15:78729921-78730898	A549	lung:	n/a	n/a
38	TBL1XR1	chr15:78729731-78730959	GM12878	blood:	n/a	n/a
39	TAF1	chr15:78730125-78730856	SK-N-SH	brain:	n/a	n/a
40	MYC	chr15:78730534-78730626	MCF-7	breast:	n/a	n/a
41	REST	chr15:78729738-78731017	A549	lung:	n/a	chr15:78730823-78730836 chr15:78730527-78730540
42	HCFC1	chr15:78729467-78732274	Hela-S3	cervix:	n/a	n/a
43	BCLAF1	chr15:78729866-78730812	GM12878	blood:	n/a	chr15:78730387-78730396 chr15:78730444-78730453 chr15:78730637-78730650
44	MAX	chr15:78729609-78731657	A549	lung:	n/a	chr15:78730153-78730162 chr15:78731240-78731250
45	SP1	chr15:78729866-78730998	A549	lung:	n/a	chr15:78730387-78730396 chr15:78730444-78730453 chr15:78730443-78730455 chr15:78730388-78730397 chr15:78730386-78730397 chr15:78730443-78730455 chr15:78730386-78730398 chr15:78730647-78730656 chr15:78730444-78730458 chr15:78730386-78730398
46	POLR2A	chr15:78729503-78730865	SK-N-SH	brain:	n/a	n/a
47	TBP	chr15:78729863-78730881	H1-hESC	embryonic stem cell:	n/a	n/a
48	TCF12	chr15:78729924-78730749	A549	lung:	n/a	n/a
49	ELK1	chr15:78729936-78730694	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr15:78729765-78730840	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:75745051..75745706-chr15:78730212..78731009,2	Hela-S3	cervix:
2	chr15:78590148..78593808-chr15:78728453..78731736,7	MCF-7	breast:
3	chr15:78587653..78594388-chr15:78727556..78733158,9	MCF-7	breast:
4	chr15:78582861..78585350-chr15:78727780..78730750,2	MCF-7	breast:
5	chr10:33247220..33247800-chr15:78730479..78731065,2	Hela-S3	cervix:
6	chr15:78556252..78558079-chr15:78730194..78731709,2	MCF-7	breast:
7	chr15:78631296..78634136-chr15:78730282..78731921,2	MCF-7	breast:
8	chr15:78730255..78731235-chr2:3383317..3383831,2	Hela-S3	cervix:
9	chr15:78730134..78730654-chr6:34204413..34205121,2	Hela-S3	cervix:
10	chr15:78590258..78594216-chr15:78729143..78732539,8	K562	blood:
11	chr15:78728533..78731605-chr15:78775460..78778377,3	K562	blood:
12	chr15:78730329..78731193-chr7:140178773..140179661,2	Hela-S3	cervix:
13	chr15:78589125..78595669-chr15:78728604..78731599,7	K562	blood:
14	chr15:78728558..78732848-chr15:78754139..78757790,4	K562	blood:
15	chr15:78729839..78731255-chr19:49122215..49122974,3	NB4	blood:
16	chr15:78729933..78731610-chr15:78832734..78835693,2	MCF-7	breast:

Variant related genes	Relation type
IREB2	TF binding region
ENSG00000229656	Chromatin interaction
ENSG00000041357	Chromatin interaction
ENSG00000170345	Chromatin interaction
ENSG00000136381	Chromatin interaction
ENSG00000259562	Chromatin interaction
ENSG00000063177	Chromatin interaction
ENSG00000259708	Chromatin interaction
ENSG00000063176	Chromatin interaction
ENSG00000171853	Chromatin interaction
ENSG00000133606	Chromatin interaction
ENSG00000137309	Chromatin interaction
ENSG00000166426	Chromatin interaction
ENSG00000140395	Chromatin interaction
ENSG00000140403	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10519198	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072762	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072765	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11639224	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12899131	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909921	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12910090	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1847529	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036532	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568498	0.92[EUR][1000 genomes]
rs2568500	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2656058	0.92[EUR][1000 genomes]
rs2869046	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4390557	0.87[EUR][1000 genomes]
rs4436747	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8041628	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
3	nsv833063	chr15:78605215-78754945	Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs954144	CHRNA5	cis	Heart Left Ventricle	GTEx
rs954144	CHRNA5	cis	Nerve Tibial	GTEx
rs954144	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs954144	RP11-650L12.2	cis	lung	GTEx
rs954144	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs954144	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs954144	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs954144	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs954144	CHRNA5	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78729400-78730800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr15:78729400-78731800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:78729600-78730600	Active TSS	Brain Germinal Matrix	brain
4	chr15:78729600-78731200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:78729600-78731400	Active TSS	Brain Substantia Nigra	brain
6	chr15:78729600-78731400	Active TSS	Thymus	Thymus
7	chr15:78729600-78731600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr15:78729600-78731600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:78729600-78731600	Active TSS	Aorta	Aorta
10	chr15:78729600-78731600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr15:78729600-78731600	Active TSS	Lung	lung
12	chr15:78729600-78731600	Active TSS	Right Ventricle	heart
13	chr15:78729600-78731800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:78729600-78731800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:78729600-78731800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:78729600-78731800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:78729600-78732000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:78729600-78732000	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr15:78729600-78732000	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr15:78729600-78732000	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr15:78729600-78732000	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr15:78729600-78732000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:78729600-78732000	Active TSS	Psoas Muscle	Psoas
24	chr15:78729600-78732000	Active TSS	Right Atrium	heart
25	chr15:78729600-78732200	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr15:78729600-78732200	Active TSS	H1 Cell Line	embryonic stem cell
27	chr15:78729600-78732200	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr15:78729800-78731000	Active TSS	Primary T cells from cord blood	blood
29	chr15:78729800-78731200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:78729800-78731400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr15:78729800-78731400	Active TSS	Brain Angular Gyrus	brain
32	chr15:78729800-78731400	Active TSS	Brain Hippocampus Middle	brain
33	chr15:78729800-78731400	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr15:78729800-78731400	Active TSS	Esophagus	oesophagus
35	chr15:78729800-78731400	Active TSS	Fetal Kidney	kidney
36	chr15:78729800-78731400	Active TSS	Gastric	stomach
37	chr15:78729800-78731400	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr15:78729800-78731400	Active TSS	Small Intestine	intestine
39	chr15:78729800-78731400	Active TSS	Stomach Mucosa	stomach
40	chr15:78729800-78731400	Active TSS	Stomach Smooth Muscle	stomach
41	chr15:78729800-78731600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:78729800-78731600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr15:78729800-78731600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:78729800-78731600	Active TSS	Colonic Mucosa	Colon
45	chr15:78729800-78731600	Active TSS	Fetal Brain Female	brain
46	chr15:78729800-78731600	Active TSS	Left Ventricle	heart
47	chr15:78729800-78731600	Active TSS	Ovary	ovary
48	chr15:78729800-78731800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr15:78729800-78732000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:78729800-78732000	Active TSS	A549	lung

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