Variant report

Variant	rs5745309
Chromosome Location	chr1:76261914-76261915
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:166)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:166 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:76260800-76263815	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:76249993-76263987	K562	blood:	n/a	n/a
3	JUND	chr1:76261570-76262865	SK-N-SH	brain:	n/a	n/a
4	MTA3	chr1:76261000-76263232	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:76261014-76263954	HEK293	kidney:	n/a	n/a
6	FOSL2	chr1:76261387-76261985	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:76260504-76263958	K562	blood:	n/a	n/a
8	BCL3	chr1:76260973-76263369	GM12878	blood:	n/a	n/a
9	STAT5A	chr1:76261029-76263366	GM12878	blood:	n/a	chr1:76261958-76261966
10	POLR2A	chr1:76257827-76264091	Hela-S3	cervix:	n/a	n/a
11	RUNX3	chr1:76261367-76263183	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:76260673-76263240	A549	lung:	n/a	n/a
13	SIN3AK20	chr1:76261767-76262264	A549	lung:	n/a	n/a
14	POU2F2	chr1:76261459-76263186	GM12878	blood:	n/a	n/a
15	HMGN3	chr1:76261012-76263063	K562	blood:	n/a	n/a
16	POLR2A	chr1:76260664-76263724	H1-hESC	embryonic stem cell:	n/a	n/a
17	SIN3AK20	chr1:76261420-76261924	K562	blood:	n/a	n/a
18	JUND	chr1:76261667-76263120	SK-N-SH	brain:	n/a	n/a
19	TEAD4	chr1:76260755-76263209	K562	blood:	n/a	n/a
20	POLR2A	chr1:76250010-76263479	K562	blood:	n/a	n/a
21	POLR2A	chr1:76250991-76264029	PFSK-1	brain:	n/a	n/a
22	BCL3	chr1:76261105-76263064	K562	blood:	n/a	n/a
23	POLR2A	chr1:76260562-76263803	GM12892	blood:	n/a	n/a
24	POLR2A	chr1:76260648-76263840	PBDE	blood:	n/a	n/a
25	POLR2A	chr1:76261351-76263505	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr1:76260916-76263975	HepG2	liver:	n/a	n/a
27	NFATC1	chr1:76261218-76263336	GM12878	blood:	n/a	n/a
28	ZNF263	chr1:76261536-76263224	HEK293-T-REx	kidney:	n/a	n/a
29	POLR2A	chr1:76260472-76264653	U87	brain:	n/a	n/a
30	BCL3	chr1:76261698-76263192	GM12878	blood:	n/a	n/a
31	ATF2	chr1:76261265-76263025	GM12878	blood:	n/a	n/a
32	HEY1	chr1:76261318-76261938	K562	blood:	n/a	n/a
33	POLR2A	chr1:76250033-76264125	K562	blood:	n/a	n/a
34	POLR2A	chr1:76260357-76263709	GM12892	blood:	n/a	n/a
35	TCF12	chr1:76261508-76262514	A549	lung:	n/a	n/a
36	POLR2A	chr1:76260821-76263271	K562	blood:	n/a	n/a
37	POLR2A	chr1:76260636-76263660	GM18526	blood:	n/a	n/a
38	POLR2A	chr1:76260903-76266662	SK-N-MC	brain:	n/a	n/a
39	POLR2A	chr1:76260889-76264192	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr1:76260881-76263233	GM12892	blood:	n/a	n/a
41	CREB1	chr1:76260841-76263301	K562	blood:	n/a	n/a
42	POLR2A	chr1:76260796-76263772	GM12892	blood:	n/a	n/a
43	POLR2A	chr1:76261246-76263772	PANC-1	pancreas:	n/a	n/a
44	POLR2A	chr1:76257887-76264164	HepG2	liver:	n/a	n/a
45	CHD2	chr1:76261563-76263028	Hela-S3	cervix:	n/a	n/a
46	MTA3	chr1:76260796-76263989	GM12878	blood:	n/a	n/a
47	PML	chr1:76260551-76262989	K562	blood:	n/a	n/a
48	POLR2A	chr1:76261413-76263161	Raji	blood:	n/a	n/a
49	POLR2A	chr1:76260828-76263740	GM12878	blood:	n/a	n/a
50	CCNT2	chr1:76260727-76263194	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:75819174..75821466-chr1:76259462..76262137,2	K562	blood:
2	chr1:76260266..76263027-chr1:76396916..76399571,2	K562	blood:
3	chr1:76213109..76217378-chr1:76260068..76263795,4	K562	blood:
4	chr1:76208992..76212319-chr1:76261590..76264096,3	K562	blood:
5	chr1:76257416..76260329-chr1:76260481..76263578,4	MCF-7	breast:
6	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
7	chr1:76200281..76202966-chr1:76259715..76263170,3	K562	blood:
8	chr1:76188764..76194417-chr1:76259356..76264333,14	K562	blood:
9	chr1:76196771..76202637-chr1:76258126..76262356,7	K562	blood:

No data

Variant related genes	Relation type
MSH4	TF binding region
ENSG00000137955	Chromatin interaction
ENSG00000181227	Chromatin interaction
ENSG00000178193	Chromatin interaction
ENSG00000154007	Chromatin interaction
ENSG00000117054	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10465725	1.00[CEU][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11161872	1.00[CEU][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1144329	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1144331	0.94[YRI][hapmap];0.91[AFR][1000 genomes]
rs1144333	0.92[ASW][hapmap];0.90[LWK][hapmap];0.97[MKK][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes]
rs1144337	0.92[ASW][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes]
rs1144339	0.91[AFR][1000 genomes]
rs1144341	0.91[AFR][1000 genomes]
rs1144342	0.94[YRI][hapmap];0.91[AFR][1000 genomes]
rs1146594	1.00[CEU][hapmap]
rs1146603	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[EUR][1000 genomes]
rs1146605	0.92[EUR][1000 genomes]
rs1146606	0.92[EUR][1000 genomes]
rs1146608	0.92[EUR][1000 genomes]
rs1146611	0.92[EUR][1000 genomes]
rs1146612	0.92[EUR][1000 genomes]
rs1146614	0.92[EUR][1000 genomes]
rs1146615	0.92[EUR][1000 genomes]
rs1146618	0.92[EUR][1000 genomes]
rs1146619	0.92[EUR][1000 genomes]
rs1146620	0.92[EUR][1000 genomes]
rs1146622	0.92[EUR][1000 genomes]
rs1146624	0.92[EUR][1000 genomes]
rs1146628	0.92[EUR][1000 genomes]
rs1146629	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1146641	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1146651	0.94[YRI][hapmap];0.91[AFR][1000 genomes]
rs12074938	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12079065	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12079211	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12079950	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12081631	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12086506	1.00[CEU][hapmap]
rs12089337	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs12090389	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs12093817	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12094698	0.92[EUR][1000 genomes]
rs1251273	0.91[AFR][1000 genomes]
rs1251274	0.92[ASW][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes]
rs13376397	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466817	0.92[MKK][hapmap]
rs17097567	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17097696	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs17097707	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17097710	1.00[CEU][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs3795251	0.81[YRI][hapmap]
rs55781251	0.91[EUR][1000 genomes]
rs55977041	1.00[EUR][1000 genomes]
rs56322662	1.00[EUR][1000 genomes]
rs56364153	0.91[EUR][1000 genomes]
rs57443433	1.00[EUR][1000 genomes]
rs5745392	0.94[YRI][hapmap];0.86[AFR][1000 genomes]
rs5745418	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5745496	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs5745516	1.00[CEU][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.87[YRI][hapmap]
rs5745542	0.81[YRI][hapmap]
rs57798497	1.00[EUR][1000 genomes]
rs58125729	1.00[EUR][1000 genomes]
rs59723961	1.00[EUR][1000 genomes]
rs59932454	1.00[EUR][1000 genomes]
rs60219146	0.91[EUR][1000 genomes]
rs61124994	0.84[EUR][1000 genomes]
rs61612438	1.00[EUR][1000 genomes]
rs6692903	1.00[CEU][hapmap]
rs74088996	0.91[EUR][1000 genomes]
rs74088997	0.91[EUR][1000 genomes]
rs74088999	0.91[EUR][1000 genomes]
rs74090705	0.91[EUR][1000 genomes]
rs74090716	1.00[EUR][1000 genomes]
rs74090717	1.00[EUR][1000 genomes]
rs74090720	1.00[EUR][1000 genomes]
rs74090724	1.00[EUR][1000 genomes]
rs74090726	1.00[EUR][1000 genomes]
rs74090729	1.00[EUR][1000 genomes]
rs74090734	1.00[EUR][1000 genomes]
rs74090737	1.00[EUR][1000 genomes]
rs74090744	1.00[EUR][1000 genomes]
rs7512465	1.00[EUR][1000 genomes]
rs7544911	0.84[EUR][1000 genomes]
rs815310	0.82[EUR][1000 genomes]
rs815311	0.82[EUR][1000 genomes]
rs9970840	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76254200-76263200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:76254400-76262400	Strong transcription	Placenta	Placenta
3	chr1:76254400-76265200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr1:76254800-76262400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:76254800-76262600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:76255200-76263600	Strong transcription	Fetal Lung	lung
7	chr1:76255400-76262600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:76255400-76263000	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr1:76255400-76265200	Weak transcription	Right Atrium	heart
10	chr1:76255600-76263000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:76255600-76264000	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr1:76255800-76264000	Strong transcription	Brain Anterior Caudate	brain
13	chr1:76255800-76264200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:76255800-76264200	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:76255800-76264400	Strong transcription	Fetal Muscle Leg	muscle
16	chr1:76256000-76262400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:76256000-76262800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:76256000-76264200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:76256000-76264200	Strong transcription	Fetal Thymus	thymus
20	chr1:76256000-76264400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:76256000-76264400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:76256000-76264600	Strong transcription	Fetal Stomach	stomach
23	chr1:76256200-76262600	Strong transcription	Fetal Kidney	kidney
24	chr1:76256200-76263000	Strong transcription	Ovary	ovary
25	chr1:76256400-76262400	Strong transcription	Fetal Brain Female	brain
26	chr1:76256400-76262800	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:76256400-76262800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:76256400-76264400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:76256600-76262400	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:76256600-76262600	Strong transcription	Primary B cells from cord blood	blood
31	chr1:76256600-76262600	Strong transcription	HMEC	breast
32	chr1:76256600-76263000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:76256600-76263000	Strong transcription	Colon Smooth Muscle	Colon
34	chr1:76256600-76263200	Strong transcription	Brain Angular Gyrus	brain
35	chr1:76256600-76263200	Strong transcription	Rectal Smooth Muscle	rectum
36	chr1:76256600-76263200	Strong transcription	NHLF	lung
37	chr1:76256600-76263400	Strong transcription	Adipose Nuclei	Adipose
38	chr1:76256600-76263400	Strong transcription	Stomach Smooth Muscle	stomach
39	chr1:76256600-76264000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr1:76256600-76264000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:76256600-76264200	Strong transcription	Brain Cingulate Gyrus	brain
42	chr1:76256600-76264600	Strong transcription	Primary B cells from peripheral blood	blood
43	chr1:76256600-76265000	Strong transcription	Primary T cells from cord blood	blood
44	chr1:76256800-76262200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:76256800-76262400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr1:76256800-76262400	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:76256800-76262400	Strong transcription	NHDF-Ad	bronchial
48	chr1:76256800-76263000	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr1:76256800-76263000	Strong transcription	Colonic Mucosa	Colon
50	chr1:76256800-76263200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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