Variant report

Variant	rs2744909
Chromosome Location	chr1:71521077-71521078
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:71520382-71521244	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:71519697-71521224	U87	brain:	n/a	n/a
3	POLR2A	chr1:71518549-71523144	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:71519204-71521209	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr1:71520511-71526660	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr1:71518581-71521507	GM12891	blood:	n/a	n/a
7	POLR2A	chr1:71519828-71521545	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr1:71519228-71521083	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr1:71518500-71525451	GM12878	blood:	n/a	n/a
10	MTA3	chr1:71519193-71521241	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:71518529-71521641	GM12891	blood:	n/a	n/a
12	POLR2A	chr1:71521064-71521502	GM12892	blood:	n/a	n/a
13	POLR2A	chr1:71519266-71521648	GM12892	blood:	n/a	n/a
14	POLR2A	chr1:71519322-71521551	K562	blood:	n/a	n/a
15	POLR2A	chr1:71518564-71521493	GM12892	blood:	n/a	n/a
16	POLR2A	chr1:71519186-71521259	A549	lung:	n/a	n/a
17	POLR2A	chr1:71519696-71521224	U87	brain:	n/a	n/a
18	NFATC1	chr1:71518743-71521240	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:71519592-71521505	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr1:71518050-71545780	K562	blood:	n/a	n/a
21	POLR2A	chr1:71519304-71521335	HL-60	blood:	n/a	n/a
22	POLR2A	chr1:71519541-71521146	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr1:71518523-71521648	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr1:71519729-71521535	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr1:71518736-71521832	GM19193	blood:	n/a	n/a
26	POLR2A	chr1:71518593-71522462	GM18505	blood:	n/a	n/a
27	POLR2A	chr1:71519164-71522437	HepG2	liver:	n/a	n/a
28	POLR2A	chr1:71519239-71521092	GM12891	blood:	n/a	n/a
29	POLR2A	chr1:71518634-71521661	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:71519828-71521516	U87	brain:	n/a	n/a
31	POLR2A	chr1:71517495-71528843	HepG2	liver:	n/a	n/a
32	POLR2A	chr1:71519484-71521733	K562	blood:	n/a	n/a
33	POLR2A	chr1:71518600-71521594	GM12891	blood:	n/a	n/a
34	CEBPB	chr1:71521029-71521240	HepG2	liver:	n/a	n/a
35	POLR2A	chr1:71519184-71521518	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr1:71519834-71521684	U87	brain:	n/a	n/a
37	POLR2A	chr1:71519258-71521668	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr1:71520665-71521346	GM12892	blood:	n/a	n/a
39	POLR2A	chr1:71519949-71521210	HCT-116	colon:	n/a	n/a
40	NFATC1	chr1:71519147-71521215	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:71520775-71521189	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr1:71520983-71521556	GM12892	blood:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:71389776..71391612-chr1:71519550..71521085,2	K562	blood:

No data

Variant related genes	Relation type
ZRANB2-AS1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10493482	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11577923	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11578414	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11800532	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11801478	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11808123	0.81[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12402425	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12409826	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1418448	0.92[EUR][1000 genomes]
rs17090804	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17090955	0.81[AMR][1000 genomes]
rs2744901	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2744903	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2796200	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2817867	0.93[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57667850	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59019236	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6699719	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72942304	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7528792	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7545836	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7554527	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9425051	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546472	chr1:71432984-71541003	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	555 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71513600-71533600	Weak transcription	Lung	lung
2	chr1:71514000-71525000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:71514000-71527400	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:71514000-71530600	Weak transcription	Ovary	ovary
5	chr1:71514000-71533600	Weak transcription	Pancreas	Pancrea
6	chr1:71514000-71533600	Weak transcription	Right Ventricle	heart
7	chr1:71514200-71524200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:71514200-71533600	Weak transcription	Spleen	Spleen
9	chr1:71514400-71524400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:71515800-71521400	Weak transcription	Adipose Nuclei	Adipose
11	chr1:71515800-71522400	Weak transcription	Liver	Liver
12	chr1:71515800-71522800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:71515800-71523200	Weak transcription	Dnd41	blood
14	chr1:71515800-71524600	Weak transcription	Fetal Brain Female	brain
15	chr1:71515800-71524800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:71515800-71525000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:71515800-71525200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:71515800-71526000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:71515800-71541000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:71516000-71524400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:71516800-71522000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:71517000-71522000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:71517000-71522200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:71517000-71522800	Weak transcription	Fetal Thymus	thymus
25	chr1:71517000-71526000	Weak transcription	Thymus	Thymus
26	chr1:71517200-71522600	Weak transcription	Primary T cells from cord blood	blood
27	chr1:71517200-71523200	Weak transcription	K562	blood
28	chr1:71517400-71522000	Weak transcription	Primary B cells from cord blood	blood
29	chr1:71517600-71523000	Weak transcription	Osteobl	bone
30	chr1:71517600-71524400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:71517600-71525000	Weak transcription	NHDF-Ad	bronchial
32	chr1:71518000-71523400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:71518200-71522000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:71518200-71522000	Weak transcription	HMEC	breast
35	chr1:71518200-71523600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr1:71518200-71523800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:71518600-71522000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:71518600-71523000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:71518800-71522200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr1:71518800-71523600	Weak transcription	Fetal Lung	lung
41	chr1:71518800-71524400	Weak transcription	Brain Hippocampus Middle	brain
42	chr1:71519000-71522200	Weak transcription	GM12878-XiMat	blood
43	chr1:71519000-71522600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr1:71519000-71522600	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr1:71519000-71523800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:71519000-71526200	Weak transcription	Brain Substantia Nigra	brain
47	chr1:71519000-71530200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:71519200-71523000	Weak transcription	A549	lung
49	chr1:71519200-71523200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:71519200-71525000	Weak transcription	HUVEC	blood vessel

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