Variant report

Variant	rs12936249
Chromosome Location	chr17:20883186-20883187
allele	A/C
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	TAL1	chr17:20883028-20883440	K562	blood:	n/a	n/a
2	GATA1	chr17:20882868-20883463	K562	blood:	n/a	chr17:20883258-20883268 chr17:20883204-20883215
3	ATF1	chr17:20883000-20883363	K562	blood:	n/a	n/a
4	SPI1	chr17:20882989-20883199	K562	blood:	n/a	n/a
5	TEAD4	chr17:20882972-20883515	K562	blood:	n/a	n/a
6	PML	chr17:20883004-20883464	K562	blood:	n/a	n/a
7	CEBPD	chr17:20883049-20883400	K562	blood:	n/a	n/a
8	POLR2A	chr17:20883068-20883309	K562	blood:	n/a	n/a
9	GATA2	chr17:20882978-20883400	K562	blood:	n/a	chr17:20883258-20883268 chr17:20883204-20883215
10	GATA2	chr17:20882953-20883435	K562	blood:	n/a	chr17:20883258-20883268 chr17:20883204-20883215
11	GATA3	chr17:20882953-20883293	T-47D	breast:	n/a	chr17:20883258-20883268 chr17:20883204-20883215
12	ZMIZ1	chr17:20883082-20883391	K562	blood:	n/a	n/a
13	GATA2	chr17:20882943-20883407	HUVEC	blood vessel:	n/a	chr17:20883258-20883268 chr17:20883204-20883215
14	JUND	chr17:20882997-20883385	K562	blood:	n/a	n/a
15	GATA3	chr17:20882982-20883295	MCF-7	breast:	n/a	chr17:20883258-20883268 chr17:20883204-20883215
16	MAZ	chr17:20883084-20883306	K562	blood:	n/a	n/a
17	TEAD4	chr17:20883019-20883446	K562	blood:	n/a	n/a
18	RCOR1	chr17:20882998-20883434	K562	blood:	n/a	n/a
19	MAX	chr17:20883018-20883251	K562	blood:	n/a	n/a
20	BHLHE40	chr17:20883062-20883311	K562	blood:	n/a	n/a
21	GABPA	chr17:20883085-20883295	K562	blood:	n/a	n/a
22	EP300	chr17:20882977-20883358	K562	blood:	n/a	n/a
23	POLR2A	chr17:20883079-20883385	K562	blood:	n/a	n/a
24	CCNT2	chr17:20883006-20883323	K562	blood:	n/a	n/a
25	STAT5A	chr17:20883099-20883414	K562	blood:	n/a	chr17:20883196-20883208
26	REST	chr17:20883061-20883220	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20839289..20841675-chr17:20882909..20885590,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DHRS7B-4	chr17:20882997-20883551	ENSG00000264660.1

Variant related genes	Relation type
ENSG00000263729	TF binding region
ENSG00000266009	TF binding region
ENSG00000265099	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1044410	0.80[ASN][1000 genomes]
rs1044414	0.80[ASN][1000 genomes]
rs1044420	0.80[ASN][1000 genomes]
rs11204328	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11650829	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11651632	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11654347	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11654680	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655364	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655562	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11658822	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11658914	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11659113	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11871167	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12600604	0.93[ASN][1000 genomes]
rs1531567	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364332	0.80[ASN][1000 genomes]
rs2364333	0.80[ASN][1000 genomes]
rs28419675	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28595150	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985813	0.82[ASN][1000 genomes]
rs4985941	0.87[ASN][1000 genomes]
rs4985946	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985947	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985948	0.93[ASN][1000 genomes]
rs4985949	0.92[ASN][1000 genomes]
rs4985952	0.92[ASN][1000 genomes]
rs4985953	0.85[ASN][1000 genomes]
rs4985954	0.85[ASN][1000 genomes]
rs4985955	0.85[ASN][1000 genomes]
rs55730423	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55749232	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55985304	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62056767	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6650606	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6650607	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7213253	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7216090	0.82[ASN][1000 genomes]
rs7220023	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7223388	0.89[ASN][1000 genomes]
rs8075790	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8076078	0.93[ASN][1000 genomes]
rs8082210	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880652	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs880654	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs899334	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs899335	0.85[ASN][1000 genomes]
rs899336	0.85[ASN][1000 genomes]
rs899338	0.85[ASN][1000 genomes]
rs961004	0.93[ASN][1000 genomes]
rs9896416	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9897434	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv1064365	chr17:20801739-20890716	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv2006	chr17:20846763-20892730	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12936249	RP11-344E13.3	cis	Whole Blood	GTEx
rs12936249	RP11-344E13.3	cis	Artery Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20848200-20896600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:20862600-20890800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr17:20866000-20886600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr17:20868000-20884800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:20871800-20886800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr17:20873200-20886400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr17:20873200-20890200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr17:20874600-20896600	Weak transcription	Spleen	Spleen
9	chr17:20881200-20883400	Enhancers	Pancreas	Pancrea
10	chr17:20881400-20883200	Weak transcription	HepG2	liver
11	chr17:20881400-20896200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr17:20882000-20883200	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr17:20882200-20886600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr17:20882600-20883200	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr17:20882600-20883800	Enhancers	K562	blood
16	chr17:20882600-20885000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr17:20882800-20883400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr17:20882800-20883400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:20882800-20883600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr17:20882800-20883600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr17:20882800-20887400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:20883000-20883200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:20883000-20883400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr17:20883000-20883400	Enhancers	NHEK	skin

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