Variant report

Variant	rs12148365
Chromosome Location	chr15:78349350-78349351
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	SPI1	chr15:78348891-78349482	HL-60	blood:	n/a	chr15:78349302-78349309 chr15:78349299-78349312 chr15:78349301-78349310 chr15:78348970-78348979 chr15:78349300-78349313
2	JUND	chr15:78349081-78349809	SK-N-SH	brain:	n/a	chr15:78349522-78349532 chr15:78349523-78349531 chr15:78349524-78349531 chr15:78349522-78349532 chr15:78349523-78349531 chr15:78349519-78349530 chr15:78349522-78349532 chr15:78349522-78349532
3	ZEB1	chr15:78348991-78349358	GM12878	blood:	n/a	chr15:78349246-78349253
4	STAT1	chr15:78349305-78349408	GM12878	blood:	n/a	n/a
5	FOSL2	chr15:78349241-78349768	A549	lung:	n/a	chr15:78349522-78349532 chr15:78349523-78349531 chr15:78349524-78349531 chr15:78349522-78349532 chr15:78349523-78349531 chr15:78349519-78349530 chr15:78349522-78349532 chr15:78349522-78349532
6	FOS	chr15:78349324-78349714	MCF10A-Er-Src	breast:	n/a	chr15:78349522-78349532 chr15:78349523-78349531 chr15:78349524-78349531 chr15:78349522-78349532 chr15:78349523-78349531 chr15:78349519-78349530 chr15:78349522-78349532 chr15:78349521-78349532 chr15:78349522-78349532
7	FOS	chr15:78349221-78349700	MCF10A-Er-Src	breast:	n/a	chr15:78349522-78349532 chr15:78349523-78349531 chr15:78349524-78349531 chr15:78349522-78349532 chr15:78349523-78349531 chr15:78349519-78349530 chr15:78349522-78349532 chr15:78349521-78349532 chr15:78349522-78349532
8	EBF1	chr15:78349248-78349472	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:78349067-78349590	HL-60	blood:	n/a	n/a
10	SPI1	chr15:78348890-78349451	GM12878	blood:	n/a	chr15:78349302-78349309 chr15:78349299-78349312 chr15:78349301-78349310 chr15:78348970-78348979 chr15:78349300-78349313
11	TCF12	chr15:78349047-78349833	SK-N-SH	brain:	n/a	n/a
12	SPI1	chr15:78348678-78349536	GM12878	blood:	n/a	chr15:78348697-78348706 chr15:78349302-78349309 chr15:78349299-78349312 chr15:78349301-78349310 chr15:78348694-78348707 chr15:78348970-78348979 chr15:78349300-78349313 chr15:78348695-78348708
13	FOS	chr15:78349276-78349713	MCF10A-Er-Src	breast:	n/a	chr15:78349522-78349532 chr15:78349523-78349531 chr15:78349524-78349531 chr15:78349522-78349532 chr15:78349523-78349531 chr15:78349519-78349530 chr15:78349522-78349532 chr15:78349521-78349532 chr15:78349522-78349532
14	ZNF263	chr15:78349119-78349409	HEK293-T-REx	kidney:	n/a	n/a
15	FOS	chr15:78348779-78349726	HUVEC	blood vessel:	n/a	chr15:78349522-78349532 chr15:78349523-78349531 chr15:78349524-78349531 chr15:78349522-78349532 chr15:78349523-78349531 chr15:78349519-78349530 chr15:78349522-78349532 chr15:78349521-78349532 chr15:78349522-78349532
16	EBF1	chr15:78349055-78349520	GM12878	blood:	n/a	n/a
17	STAT3	chr15:78349323-78349665	MCF10A-Er-Src	breast:	n/a	chr15:78349540-78349548
18	SPI1	chr15:78348403-78349533	HL-60	blood:	n/a	chr15:78348697-78348706 chr15:78349302-78349309 chr15:78349299-78349312 chr15:78349301-78349310 chr15:78348694-78348707 chr15:78348970-78348979 chr15:78349300-78349313 chr15:78348695-78348708 chr15:78348545-78348558
19	TCF12	chr15:78349010-78349818	SK-N-SH	brain:	n/a	n/a
20	JUND	chr15:78349330-78349678	Hela-S3	cervix:	n/a	chr15:78349522-78349532 chr15:78349523-78349531 chr15:78349524-78349531 chr15:78349522-78349532 chr15:78349523-78349531 chr15:78349519-78349530 chr15:78349522-78349532 chr15:78349522-78349532
21	EBF1	chr15:78349228-78349484	GM12878	blood:	n/a	n/a
22	USF2	chr15:78349348-78349685	Hela-S3	cervix:	n/a	n/a
23	RUNX3	chr15:78349033-78349467	GM12878	blood:	n/a	n/a
24	SPI1	chr15:78348850-78349451	GM12891	blood:	n/a	chr15:78349302-78349309 chr15:78349299-78349312 chr15:78349301-78349310 chr15:78348970-78348979 chr15:78349300-78349313
25	SPI1	chr15:78348891-78349426	GM12891	blood:	n/a	chr15:78349302-78349309 chr15:78349299-78349312 chr15:78349301-78349310 chr15:78348970-78348979 chr15:78349300-78349313
26	TCF3	chr15:78349107-78349439	GM12878	blood:	n/a	chr15:78349413-78349426
27	POLR2A	chr15:78348997-78349486	HL-60	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:78349349-78349399	HEEpiC	esophagus:	n/a
2	chr15:78349349-78349399	AoSMC	blood vessel:	n/a
3	chr15:78349349-78349399	GM12891	blood:	n/a
4	chr15:78349349-78349399	IMR90	lung:	fetal
5	chr15:78349349-78349399	HUVEC	blood vessel:	n/a
6	chr15:78349349-78349399	HIPEpiC	eye:	n/a
7	chr15:78349349-78349399	NHDF-neo	bronchial:	n/a
8	chr15:78349349-78349399	PrEC	prostate:	n/a
9	chr15:78349349-78349399	MCF-7	breast:	n/a
10	chr15:78349349-78349399	Jurkat	blood:	n/a
11	chr15:78349349-78349399	HCPEpiC	choroid plexus:	n/a
12	chr15:78349349-78349399	GM19239	blood:	n/a
13	chr15:78349349-78349399	Hepatocyte	liver:	n/a
14	chr15:78349349-78349399	SK-N-SH_RA	brain:	n/a
15	chr15:78349349-78349399	HCM	heart:	n/a
16	chr15:78349349-78349399	NB4	blood:	n/a
17	chr15:78349349-78349399	HMEC	breast:	n/a
18	chr15:78349349-78349399	NH-A	brain:	n/a
19	chr15:78349349-78349399	MCF10A-Er-Src	breast:	n/a
20	chr15:78349349-78349399	HRPEpiC	eye:	n/a
21	chr15:78349349-78349399	HCF	heart:	n/a
22	chr15:78349349-78349399	PFSK-1	brain:	n/a
23	chr15:78349349-78349399	HNPCEpiC	eye:	n/a
24	chr15:78349349-78349399	Caco-2	colon:	n/a
25	chr15:78349349-78349399	ProgFib	skin:	n/a
26	chr15:78349349-78349399	RPTEC	kidney:	n/a
27	chr15:78349349-78349399	T-47D	breast:	n/a
28	chr15:78349349-78349399	HAEpiC	amniotic membrane:	n/a
29	chr15:78349349-78349399	HCT-116	colon:	n/a
30	chr15:78349349-78349399	SK-N-SH	brain:	n/a
31	chr15:78349349-78349399	SAEC	small airway:	n/a
32	chr15:78349349-78349399	BE2_C	brain:	n/a
33	chr15:78349349-78349399	HepG2	liver:	n/a
34	chr15:78349349-78349399	Hela-S3	cervix:	n/a
35	chr15:78349349-78349399	HRE	kidney:	n/a
36	chr15:78349349-78349399	GM06990	blood:	n/a
37	chr15:78349349-78349399	PANC-1	pancreas:	n/a
38	chr15:78349349-78349399	AG09309	skin:	n/a
39	chr15:78349349-78349399	NT2-D1	testis:	n/a
40	chr15:78349349-78349399	A549	lung:	n/a
41	chr15:78349349-78349399	SKMC	muscle:	n/a
42	chr15:78349349-78349399	H1-hESC	embryonic stem cell:	embryo
43	chr15:78349349-78349399	K562	blood:	n/a
44	chr15:78349349-78349399	AG09319	gingival:	n/a
45	chr15:78349349-78349399	HEK293	kidney:	embryo
46	chr15:78349349-78349399	AG04449	skin:	fetal
47	chr15:78349349-78349399	BJ	skin:	n/a
48	chr15:78349349-78349399	AG10803	skin:	n/a
49	chr15:78349349-78349399	GM12878	blood:	n/a
50	chr15:78349349-78349399	ECC-1	luminal epithelium:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:78343843..78346703-chr15:78348028..78350338,4	MCF-7	breast:
2	chr15:78332545..78335150-chr15:78348925..78351809,2	MCF-7	breast:
3	chr15:78347136..78350100-chr15:78350153..78352439,2	K562	blood:
4	chr15:78348877..78350623-chr15:78357626..78359289,2	MCF-7	breast:
5	chr15:78346803..78349725-chr15:78352567..78355144,4	MCF-7	breast:
6	chr15:78347928..78349510-chr15:78375068..78376834,2	MCF-7	breast:
7	chr15:78349057..78351181-chr15:78355340..78357401,2	MCF-7	breast:

Variant related genes	Relation type
TBC1D2B	TF binding region
TBC1D2B	CpG island
ENSG00000167202	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1004855	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs10519181	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs11072716	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs11631578	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11634607	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11638311	0.81[ASN][1000 genomes]
rs11852768	0.97[ASN][1000 genomes]
rs12442213	0.83[CHB][hapmap]
rs12591418	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12594823	0.91[CHB][hapmap];0.97[CHD][hapmap]
rs12899061	0.94[ASN][1000 genomes]
rs12901812	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs12907701	0.95[ASN][1000 genomes]
rs12907814	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12911332	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs12916362	0.95[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs1348257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1442293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1837913	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1992470	0.91[CHB][hapmap]
rs2028546	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2044099	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2241885	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs2867985	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2903702	0.96[ASN][1000 genomes]
rs3803380	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs4395040	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap]
rs4886553	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886554	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886555	0.98[ASN][1000 genomes]
rs4886994	0.86[ASN][1000 genomes]
rs4886995	0.83[CHB][hapmap]
rs4886996	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs4886999	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs4887000	0.95[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs55704745	0.81[ASN][1000 genomes]
rs56317829	0.95[ASN][1000 genomes]
rs57220134	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs58578288	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62011511	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166819	0.97[ASN][1000 genomes]
rs7170746	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7173128	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7174489	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap]
rs7181594	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8029562	0.92[ASN][1000 genomes]
rs8030873	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9047	0.98[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	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	nsv1051558	chr15:78315542-78364947	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12148365	HEXA	cis	parietal	SCAN
rs12148365	CLK3	cis	cerebellum	SCAN
rs12148365	MORF4L1	cis	parietal	SCAN
rs12148365	ISL2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78296200-78358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:78309200-78354200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:78327600-78351400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:78343200-78354200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:78344400-78352000	Genic enhancers	Fetal Intestine Small	intestine
6	chr15:78344800-78357600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:78344800-78359800	Weak transcription	Fetal Brain Female	brain
8	chr15:78345000-78352000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:78345000-78354200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:78345200-78351400	Weak transcription	Fetal Kidney	kidney
11	chr15:78345600-78351800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr15:78346200-78350000	Enhancers	Liver	Liver
13	chr15:78346200-78354200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:78346400-78349600	Enhancers	Brain Hippocampus Middle	brain
15	chr15:78346400-78353200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr15:78346400-78354200	Enhancers	Primary T cells fromperipheralblood	blood
17	chr15:78346400-78356600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:78346600-78349600	Enhancers	Brain Substantia Nigra	brain
19	chr15:78346600-78353000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:78346600-78354200	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr15:78346800-78354400	Enhancers	Primary B cells from cord blood	blood
22	chr15:78347000-78349600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:78347000-78349600	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr15:78347000-78350400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr15:78347000-78351200	Enhancers	HSMM	muscle
26	chr15:78347000-78351400	Enhancers	Fetal Muscle Leg	muscle
27	chr15:78347000-78352800	Enhancers	Stomach Mucosa	stomach
28	chr15:78347000-78357400	Enhancers	Fetal Thymus	thymus
29	chr15:78347200-78352200	Enhancers	Small Intestine	intestine
30	chr15:78347400-78349400	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr15:78347400-78349400	Enhancers	Esophagus	oesophagus
32	chr15:78347400-78349400	Enhancers	Psoas Muscle	Psoas
33	chr15:78347400-78349400	Enhancers	Spleen	Spleen
34	chr15:78347400-78350000	Enhancers	Duodenum Mucosa	Duodenum
35	chr15:78347400-78350000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr15:78347400-78350200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:78347400-78350400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:78347400-78350800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr15:78347400-78351400	Enhancers	HSMMtube	muscle
40	chr15:78347400-78352200	Enhancers	Primary hematopoietic stem cells	blood
41	chr15:78347400-78352400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:78347400-78352400	Enhancers	Fetal Intestine Large	intestine
43	chr15:78347400-78352600	Enhancers	Brain Anterior Caudate	brain
44	chr15:78347400-78354000	Enhancers	NHDF-Ad	bronchial
45	chr15:78347400-78354200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr15:78347400-78354200	Enhancers	Adipose Nuclei	Adipose
47	chr15:78347400-78367800	Enhancers	Placenta	Placenta
48	chr15:78347600-78349800	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr15:78347600-78352200	Enhancers	Colon Smooth Muscle	Colon
50	chr15:78347600-78352600	Enhancers	Brain Cingulate Gyrus	brain

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