Variant report

Variant	rs12914047
Chromosome Location	chr15:52970993-52970994
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	TCF7L2	chr15:52970986-52971274	Hela-S3	cervix:	n/a	n/a
2	CREB1	chr15:52970220-52971959	HepG2	liver:	n/a	n/a
3	CTCF	chr15:52970960-52971110	HRPEpiC	eye:	n/a	n/a
4	GABPA	chr15:52970716-52971174	K562	blood:	n/a	chr15:52970744-52970753
5	POLR2A	chr15:52970877-52971119	A549	lung:	n/a	n/a
6	ELF1	chr15:52970726-52971071	K562	blood:	n/a	chr15:52970870-52970883 chr15:52970922-52970934
7	JUND	chr15:52970774-52971049	H1-hESC	embryonic stem cell:	n/a	n/a
8	ELF1	chr15:52970747-52971368	GM12878	blood:	n/a	chr15:52970870-52970883 chr15:52971350-52971362 chr15:52971263-52971275 chr15:52970922-52970934
9	POLR2A	chr15:52969910-52971897	MCF10A-Er-Src	breast:	n/a	n/a
10	CTCF	chr15:52970980-52971130	RPTEC	kidney:	n/a	chr15:52971105-52971123
11	FOSL2	chr15:52970276-52972012	MCF-7	breast:	n/a	chr15:52971115-52971127 chr15:52971116-52971126 chr15:52971708-52971722 chr15:52970749-52970758
12	FOXA2	chr15:52970271-52971236	A549	lung:	n/a	n/a
13	MAX	chr15:52970726-52971966	SK-N-SH	brain:	n/a	chr15:52971590-52971603 chr15:52971591-52971602 chr15:52971592-52971601 chr15:52971592-52971601 chr15:52971590-52971603 chr15:52971590-52971603
14	POLR2A	chr15:52970599-52971861	HUVEC	blood vessel:	n/a	n/a
15	PML	chr15:52970451-52972018	MCF-7	breast:	n/a	n/a
16	TFAP2A	chr15:52970490-52971969	Hela-S3	cervix:	n/a	chr15:52971691-52971702 chr15:52971692-52971700 chr15:52971693-52971701 chr15:52971691-52971702 chr15:52971430-52971438 chr15:52971691-52971702 chr15:52971693-52971701 chr15:52971691-52971702 chr15:52971430-52971438 chr15:52971692-52971700 chr15:52971692-52971700 chr15:52971693-52971701 chr15:52971691-52971702 chr15:52971430-52971438
17	GATA3	chr15:52970179-52972282	MCF-7	breast:	n/a	chr15:52971629-52971639
18	TCF12	chr15:52970611-52972044	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr15:52970216-52971974	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr15:52970513-52971985	H1-hESC	embryonic stem cell:	n/a	n/a
21	TBP	chr15:52970445-52971916	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr15:52970861-52972001	H1-neurons	neurons:	n/a	n/a
23	MAX	chr15:52970079-52972574	MCF-7	breast:	n/a	chr15:52971590-52971603 chr15:52971591-52971602 chr15:52971592-52971601 chr15:52971592-52971601 chr15:52971590-52971603 chr15:52971590-52971603 chr15:52972284-52972293
24	YY1	chr15:52970918-52971801	K562	blood:	n/a	chr15:52971643-52971657 chr15:52970989-52971000 chr15:52971744-52971766 chr15:52971392-52971401 chr15:52970989-52970998 chr15:52971242-52971253 chr15:52971757-52971765 chr15:52971267-52971281
25	SIN3A	chr15:52970016-52972473	H1-hESC	embryonic stem cell:	n/a	chr15:52970877-52970890 chr15:52970919-52970932 chr15:52970845-52970856 chr15:52971384-52971395 chr15:52971685-52971698
26	POLR2A	chr15:52970611-52972137	MCF-7	breast:	n/a	n/a
27	RFX5	chr15:52969780-52972825	SK-N-SH	brain:	n/a	chr15:52971597-52971612 chr15:52971667-52971682 chr15:52971667-52971682 chr15:52969927-52969935 chr15:52971666-52971683 chr15:52971667-52971682
28	REST	chr15:52970313-52971945	MCF-7	breast:	n/a	chr15:52971230-52971243 chr15:52971486-52971494 chr15:52971688-52971701 chr15:52971479-52971492 chr15:52971365-52971378 chr15:52971178-52971191 chr15:52971472-52971492 chr15:52971368-52971381
29	RFX5	chr15:52970794-52971963	IMR90	lung:	n/a	chr15:52971597-52971612 chr15:52971667-52971682 chr15:52971667-52971682 chr15:52971666-52971683 chr15:52971667-52971682
30	REST	chr15:52970962-52971966	H1-neurons	neurons:	n/a	chr15:52971230-52971243 chr15:52971486-52971494 chr15:52971688-52971701 chr15:52971479-52971492 chr15:52971365-52971378 chr15:52971178-52971191 chr15:52971472-52971492 chr15:52971368-52971381
31	GABPA	chr15:52970219-52972197	MCF-7	breast:	n/a	chr15:52970744-52970753
32	HCFC1	chr15:52969381-52972517	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr15:52970810-52971229	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr15:52970832-52971166	HepG2	liver:	n/a	n/a
35	POLR2A	chr15:52970568-52971913	GM12892	blood:	n/a	n/a
36	FOXA1	chr15:52970566-52971045	T-47D	breast:	n/a	chr15:52970810-52970825
37	POLR2A	chr15:52970927-52971894	PBDE	blood:	n/a	n/a
38	FOXA2	chr15:52970609-52971041	HepG2	liver:	n/a	n/a
39	POLR2A	chr15:52970983-52971139	K562	blood:	n/a	n/a
40	POLR2A	chr15:52970267-52972272	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr15:52970678-52971863	GM12878	blood:	n/a	n/a
42	POLR2A	chr15:52970358-52971885	K562	blood:	n/a	n/a
43	TBP	chr15:52970681-52971763	HepG2	liver:	n/a	n/a
44	POLR2A	chr15:52970878-52971857	A549	lung:	n/a	n/a
45	HEY1	chr15:52970576-52971194	HepG2	liver:	n/a	chr15:52970696-52970711
46	TAF1	chr15:52970878-52971334	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr15:52969877-52971953	GM19099	blood:	n/a	n/a
48	JUND	chr15:52970862-52971357	A549	lung:	n/a	chr15:52971115-52971127 chr15:52971116-52971126
49	POLR2A	chr15:52970869-52971810	K562	blood:	n/a	n/a
50	POLR2A	chr15:52970827-52971930	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52819791..52821534-chr15:52970285..52973265,2	MCF-7	breast:
2	chr15:50645577..50647649-chr15:52968775..52972037,3	MCF-7	breast:
3	chr15:52586831..52588797-chr15:52969729..52971575,2	MCF-7	breast:
4	chr15:52859855..52863944-chr15:52968349..52971887,6	MCF-7	breast:
5	chr15:52967401..52973659-chr15:53000765..53004676,11	MCF-7	breast:
6	chr15:52968259..52973250-chr15:52997483..53005703,18	MCF-7	breast:
7	chr15:52855349..52864927-chr15:52966670..52972620,15	MCF-7	breast:
8	chr15:52942408..52952117-chr15:52965431..52973600,32	MCF-7	breast:

Variant related genes	Relation type
FAM214A	TF binding region
ENSG00000104064	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000128989	Chromatin interaction
ENSG00000128833	Chromatin interaction
ENSG00000047346	Chromatin interaction
ENSG00000197535	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10851521	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11070907	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070908	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11070909	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11633933	0.86[EUR][1000 genomes]
rs11853917	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11857150	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11858743	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12898644	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914502	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12915981	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1863512	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2414163	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2414166	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34431049	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3751614	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4774636	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4776065	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4776066	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4776068	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62023352	0.82[ASN][1000 genomes]
rs8026800	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs933860	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1049534	chr15:52903314-53022926	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12914047	KIAA1370	cis	brain	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52967400-52972400	Active TSS	Right Atrium	heart
2	chr15:52968400-52972200	Active TSS	Brain Germinal Matrix	brain
3	chr15:52968600-52972200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:52968600-52972200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:52969000-52971000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr15:52969000-52972200	Active TSS	GM12878-XiMat	blood
7	chr15:52969000-52972400	Active TSS	Psoas Muscle	Psoas
8	chr15:52969000-52972400	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr15:52969200-52971000	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr15:52969400-52972200	Active TSS	Aorta	Aorta
11	chr15:52969400-52972200	Active TSS	Fetal Intestine Small	intestine
12	chr15:52969400-52972200	Active TSS	Thymus	Thymus
13	chr15:52969600-52971800	Active TSS	Primary T cells fromperipheralblood	blood
14	chr15:52969600-52972000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:52969600-52972000	Active TSS	Fetal Thymus	thymus
16	chr15:52969600-52972200	Active TSS	Fetal Intestine Large	intestine
17	chr15:52969600-52972200	Active TSS	HMEC	breast
18	chr15:52969600-52972200	Active TSS	NHLF	lung
19	chr15:52969600-52972400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:52969600-52972400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:52969800-52971400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:52969800-52972000	Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr15:52969800-52972000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:52969800-52972200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:52969800-52972200	Active TSS	NH-A	brain
26	chr15:52969800-52972200	Active TSS	NHDF-Ad	bronchial
27	chr15:52969800-52972400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:52969800-52972400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:52969800-52972600	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr15:52969800-52972600	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr15:52969800-52972600	Active TSS	Fetal Kidney	kidney
32	chr15:52969800-52972600	Active TSS	Right Ventricle	heart
33	chr15:52969800-52973000	Active TSS	HSMMtube	muscle
34	chr15:52970000-52971200	Active TSS	Fetal Heart	heart
35	chr15:52970000-52972000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:52970000-52972000	Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr15:52970000-52972000	Active TSS	Lung	lung
38	chr15:52970000-52972000	Active TSS	Small Intestine	intestine
39	chr15:52970000-52972000	Active TSS	Stomach Mucosa	stomach
40	chr15:52970000-52972000	Active TSS	HSMM	muscle
41	chr15:52970000-52972200	Active TSS	H9 Cell Line	embryonic stem cell
42	chr15:52970000-52972200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:52970000-52972200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:52970000-52972200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr15:52970000-52972200	Active TSS	Ovary	ovary
46	chr15:52970000-52972200	Active TSS	Pancreas	Pancrea
47	chr15:52970000-52972200	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr15:52970000-52972400	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr15:52970000-52972400	Active TSS	Left Ventricle	heart
50	chr15:52970000-52972600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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