Variant report

Variant	rs12899522
Chromosome Location	chr15:83738054-83738055
allele	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	FOS	chr15:83737988-83738365	K562	blood:	n/a	n/a
2	CHD2	chr15:83737959-83738316	H1-hESC	embryonic stem cell:	n/a	n/a
3	SP1	chr15:83737901-83738419	K562	blood:	n/a	n/a
4	SP1	chr15:83737907-83738464	GM12878	blood:	n/a	n/a
5	MAFK	chr15:83737967-83738349	IMR90	lung:	n/a	chr15:83738134-83738149 chr15:83738158-83738173 chr15:83738182-83738197 chr15:83738110-83738125
6	NFYA	chr15:83737941-83738500	K562	blood:	n/a	chr15:83738182-83738200 chr15:83738230-83738248 chr15:83738206-83738224
7	CBX3	chr15:83737778-83738573	K562	blood:	n/a	n/a
8	MAFK	chr15:83737973-83738338	HepG2	liver:	n/a	chr15:83738134-83738149 chr15:83738158-83738173 chr15:83738182-83738197 chr15:83738110-83738125
9	ELF1	chr15:83737827-83738235	K562	blood:	n/a	chr15:83738061-83738074
10	MAFK	chr15:83738054-83738311	K562	blood:	n/a	chr15:83738134-83738149 chr15:83738158-83738173 chr15:83738182-83738197 chr15:83738110-83738125
11	EGR1	chr15:83737881-83738174	K562	blood:	n/a	n/a
12	NFYB	chr15:83737914-83738417	K562	blood:	n/a	chr15:83738212-83738227 chr15:83738140-83738155 chr15:83738164-83738179 chr15:83738188-83738203
13	MAFK	chr15:83738053-83738313	H1-hESC	embryonic stem cell:	n/a	chr15:83738134-83738149 chr15:83738158-83738173 chr15:83738182-83738197 chr15:83738110-83738125
14	SP1	chr15:83737859-83738509	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAFF	chr15:83738033-83738256	K562	blood:	n/a	chr15:83738132-83738150
16	NFYB	chr15:83737786-83738593	GM12878	blood:	n/a	chr15:83738212-83738227 chr15:83738140-83738155 chr15:83738164-83738179 chr15:83738188-83738203
17	EGR1	chr15:83737824-83738153	K562	blood:	n/a	n/a
18	MAFK	chr15:83737969-83738363	HepG2	liver:	n/a	chr15:83738134-83738149 chr15:83738158-83738173 chr15:83738182-83738197 chr15:83738110-83738125
19	SP1	chr15:83737865-83738497	H1-hESC	embryonic stem cell:	n/a	n/a
20	ELF1	chr15:83738035-83738171	HepG2	liver:	n/a	chr15:83738061-83738074
21	SP1	chr15:83737931-83738464	A549	lung:	n/a	n/a
22	SP1	chr15:83737879-83738447	A549	lung:	n/a	n/a
23	IRF1	chr15:83737975-83738198	K562	blood:	n/a	n/a
24	SP1	chr15:83737883-83738415	GM12878	blood:	n/a	n/a
25	NFYA	chr15:83737988-83738405	Hela-S3	cervix:	n/a	chr15:83738182-83738200 chr15:83738230-83738248 chr15:83738206-83738224
26	MAFF	chr15:83737984-83738367	HepG2	liver:	n/a	chr15:83738132-83738150
27	NFYB	chr15:83737943-83738399	Hela-S3	cervix:	n/a	chr15:83738212-83738227 chr15:83738140-83738155 chr15:83738164-83738179 chr15:83738188-83738203

No.	Distal block	Cell Line	Cell type
1	chr15:83733297..83738085-chr15:83874642..83880991,12	MCF-7	breast:
2	chr15:83679205..83686226-chr15:83733349..83739878,12	K562	blood:
3	chr15:83734015..83735613-chr15:83737499..83739038,2	K562	blood:
4	chr15:83678535..83684480-chr15:83731660..83738533,12	MCF-7	breast:
5	chr15:83731075..83738271-chr15:83771545..83781798,12	K562	blood:
6	chr15:83679004..83681789-chr15:83733343..83738150,8	MCF-7	breast:
7	chr15:83233945..83235595-chr15:83736586..83738485,2	K562	blood:

Variant related genes	Relation type
BTBD1	TF binding region
ENSG00000166503	Chromatin interaction
ENSG00000260608	Chromatin interaction
ENSG00000136404	Chromatin interaction
ENSG00000169609	Chromatin interaction
ENSG00000249214	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10400812	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11858074	0.88[ASN][1000 genomes]
rs12439782	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12592391	0.88[ASN][1000 genomes]
rs12900411	0.88[ASN][1000 genomes]
rs12901811	0.88[ASN][1000 genomes]
rs12902721	0.85[ASN][1000 genomes]
rs12903066	0.88[ASN][1000 genomes]
rs12904695	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12906027	0.88[ASN][1000 genomes]
rs12906626	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12907032	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12911706	0.88[ASN][1000 genomes]
rs12911891	0.88[ASN][1000 genomes]
rs12913130	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12917594	0.89[ASN][1000 genomes]
rs13329195	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13329269	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17158127	0.88[ASN][1000 genomes]
rs17507300	0.91[ASN][1000 genomes]
rs2084839	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2381030	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28485801	0.89[ASN][1000 genomes]
rs28580677	0.92[ASN][1000 genomes]
rs3087804	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34869943	0.85[ASN][1000 genomes]
rs35207081	0.88[ASN][1000 genomes]
rs35627116	0.89[ASN][1000 genomes]
rs36038412	0.88[ASN][1000 genomes]
rs4079029	0.92[ASN][1000 genomes]
rs61375537	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6603044	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6603046	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66606849	0.88[ASN][1000 genomes]
rs67482297	0.88[ASN][1000 genomes]
rs67822554	0.88[ASN][1000 genomes]
rs7163516	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7166645	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7170547	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7172665	0.92[EUR][1000 genomes]
rs7177599	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7181169	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs750214	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7757	0.88[ASN][1000 genomes]
rs8031896	0.91[ASN][1000 genomes]
rs8040457	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8040998	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9646239	0.88[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	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12899522	HDGFRP3	Cis_1M	lymphoblastoid	RTeQTL
rs12899522	BTBD1	cis	Nerve Tibial	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83736600-83738800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr15:83736600-83739000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:83736800-83738800	Weak transcription	Osteobl	bone
4	chr15:83736800-83739200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:83737000-83738600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:83737000-83739800	Weak transcription	Fetal Muscle Leg	muscle
7	chr15:83737400-83738600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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