Variant report

Variant	rs947086
Chromosome Location	chr1:228328743-228328744
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	POLR2A	chr1:228327199-228329184	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:228328532-228328868	GM12878	blood:	n/a	n/a
3	SMARCB1	chr1:228327329-228328854	Hela-S3	cervix:	n/a	n/a
4	UBTF	chr1:228327292-228329537	K562	blood:	n/a	n/a
5	MAX	chr1:228327196-228329894	K562	blood:	n/a	chr1:228328264-228328274 chr1:228327695-228327705
6	JUN	chr1:228327040-228329256	K562	blood:	n/a	chr1:228327920-228327933
7	POLR2A	chr1:228327060-228329092	K562	blood:	n/a	n/a
8	MXI1	chr1:228327097-228329751	IMR90	lung:	n/a	n/a
9	RCOR1	chr1:228328713-228328761	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:228327201-228328861	HepG2	liver:	n/a	n/a
11	WRNIP1	chr1:228328437-228330112	GM12878	blood:	n/a	n/a
12	ELF1	chr1:228327146-228329456	GM12878	blood:	n/a	chr1:228328261-228328273 chr1:228327699-228327711 chr1:228328106-228328115
13	POLR2A	chr1:228327209-228329992	K562	blood:	n/a	n/a
14	MXI1	chr1:228327403-228329679	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:228327346-228328972	GM12878	blood:	n/a	n/a
16	MXI1	chr1:228328658-228328895	K562	blood:	n/a	n/a
17	MXI1	chr1:228327052-228329702	SK-N-SH	brain:	n/a	n/a
18	MYC	chr1:228327336-228329755	K562	blood:	n/a	chr1:228328264-228328274 chr1:228327695-228327705
19	REST	chr1:228327071-228328854	H1-neurons	neurons:	n/a	chr1:228328283-228328296 chr1:228328110-228328123 chr1:228327614-228327621 chr1:228327692-228327705
20	POLR2A	chr1:228327189-228328816	PBDE	blood:	n/a	n/a
21	POLR2A	chr1:228327198-228329161	GM12891	blood:	n/a	n/a
22	POLR2A	chr1:228327235-228329827	K562	blood:	n/a	n/a
23	MAX	chr1:228327178-228328766	A549	lung:	n/a	chr1:228328264-228328274 chr1:228327695-228327705
24	IRF1	chr1:228327247-228329497	K562	blood:	n/a	chr1:228327834-228327848 chr1:228327875-228327889 chr1:228328731-228328745 chr1:228329022-228329043 chr1:228327694-228327708 chr1:228328263-228328277
25	RUNX3	chr1:228328677-228329321	GM12878	blood:	n/a	n/a
26	CHD1	chr1:228327017-228329831	IMR90	lung:	n/a	n/a
27	POLR2A	chr1:228327114-228332328	IMR90	lung:	n/a	n/a
28	POLR2A	chr1:228328459-228328888	K562	blood:	n/a	n/a
29	POLR2A	chr1:228327239-228329943	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr1:228327324-228329296	GM18505	blood:	n/a	n/a
31	MAFK	chr1:228328443-228328765	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr1:228327129-228329167	GM19193	blood:	n/a	n/a
33	NR2F2	chr1:228327128-228329051	K562	blood:	n/a	n/a
34	SMARCC1	chr1:228327787-228328871	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr1:228327017-228328864	K562	blood:	n/a	n/a
36	MXI1	chr1:228327323-228329650	GM12878	blood:	n/a	n/a
37	MAZ	chr1:228327249-228329314	IMR90	lung:	n/a	chr1:228328264-228328274 chr1:228327695-228327705
38	POLR2A	chr1:228327038-228328868	K562	blood:	n/a	n/a
39	STAT5A	chr1:228328728-228329102	GM12878	blood:	n/a	n/a
40	HCFC1	chr1:228327120-228328753	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr1:228327142-228329234	GM12892	blood:	n/a	n/a
42	CHD1	chr1:228327337-228329387	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:228328533-228328890	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr1:228327370-228330398	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:228328562-228328881	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:228327172-228329094	H1-hESC	embryonic stem cell:	n/a	n/a
47	SIN3AK20	chr1:228327567-228328776	K562	blood:	n/a	n/a
48	SIN3A	chr1:228327238-228328750	H1-hESC	embryonic stem cell:	n/a	chr1:228328283-228328296
49	RCOR1	chr1:228328698-228328744	K562	blood:	n/a	n/a
50	E2F6	chr1:228328627-228328790	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228327365..228329534-chr1:228645028..228646794,2	MCF-7	breast:
2	chr1:228328019..228328956-chr8:93977378..93978060,2	Hela-S3	cervix:
3	chr1:228267667..228275106-chr1:228326600..228331394,10	K562	blood:
4	chr1:228328125..228328820-chr1:228353335..228354006,2	MCF-7	breast:
5	chr1:228269915..228273320-chr1:228326449..228329096,4	K562	blood:
6	chr1:228293945..228298846-chr1:228325398..228330582,13	K562	blood:
7	chr1:228290240..228294197-chr1:228325970..228329742,3	MCF-7	breast:
8	chr1:228269306..228272326-chr1:228326148..228329488,5	MCF-7	breast:
9	chr1:228294222..228297212-chr1:228327852..228330069,2	MCF-7	breast:
10	chr1:228319215..228325156-chr1:228326279..228328957,6	K562	blood:
11	chr1:228288649..228293430-chr1:228325997..228329591,7	K562	blood:
12	chr1:228327593..228329181-chr1:228644179..228646860,2	MCF-7	breast:
13	chr1:228326695..228329093-chr1:228572036..228574543,2	K562	blood:
14	chr1:228284520..228292111-chr1:228324853..228335412,14	K562	blood:
15	chr1:228286712..228292079-chr1:228327501..228330420,5	MCF-7	breast:
16	chr1:228294705..228298588-chr1:228325821..228329680,6	MCF-7	breast:
17	chr1:228327795..228330213-chr1:228593794..228595426,3	K562	blood:
18	chr1:228326053..228331395-chr1:228462710..228467617,6	K562	blood:
19	chr1:228328463..228331528-chr1:228462308..228464210,3	K562	blood:
20	chr1:228326723..228329419-chr1:228644101..228647035,3	K562	blood:
21	chr1:228269794..228271921-chr1:228327972..228330804,3	MCF-7	breast:
22	chr1:228293945..228298682-chr1:228326047..228331152,9	K562	blood:

Variant related genes	Relation type
GUK1	TF binding region
ENSG00000269934	Chromatin interaction
ENSG00000205133	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000162910	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000270104	Chromatin interaction
ENSG00000227625	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000154358	Chromatin interaction
ENSG00000154370	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000231563	Chromatin interaction
ENSG00000264944	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10916269	0.92[ASW][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap]
rs1757154	1.00[AMR][1000 genomes]
rs1771454	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs1771466	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs1771475	0.92[ASW][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap]
rs1856871	0.82[AFR][1000 genomes]
rs1934881	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1934882	0.95[YRI][hapmap];0.94[AFR][1000 genomes]
rs2313599	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4653534	0.84[AFR][1000 genomes]
rs4653535	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4653916	0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs486504	1.00[AMR][1000 genomes]
rs6667424	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6686210	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7534419	0.86[YRI][hapmap]
rs822728	0.92[ASW][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap]
rs822729	0.86[YRI][hapmap]
rs822731	0.92[ASW][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap]
rs822732	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs822741	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs849750	0.92[ASW][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap]
rs947083	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS 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	187 gene(s)	inside rSNPs	diseases
3	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
4	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
5	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
6	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
8	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
9	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
10	nsv873256	chr1:228322826-228359775	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
11	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
12	esv3398542	chr1:228326754-228329302	Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv549288	chr1:228327659-228363750	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
14	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228327000-228328800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr1:228327000-228328800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:228327000-228328800	Active TSS	Brain Angular Gyrus	brain
4	chr1:228327000-228329000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:228327000-228329000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:228327000-228329200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:228327000-228329200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:228327000-228329400	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr1:228327000-228329400	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr1:228327200-228328800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr1:228327200-228328800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:228327200-228328800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:228327200-228328800	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr1:228327200-228328800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:228327200-228328800	Active TSS	Brain Hippocampus Middle	brain
16	chr1:228327200-228328800	Active TSS	Colon Smooth Muscle	Colon
17	chr1:228327200-228328800	Active TSS	Right Ventricle	heart
18	chr1:228327200-228328800	Active TSS	Stomach Mucosa	stomach
19	chr1:228327200-228329000	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr1:228327200-228329000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr1:228327200-228329000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:228327200-228329000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:228327200-228329000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:228327200-228329000	Active TSS	Fetal Kidney	kidney
25	chr1:228327200-228329000	Active TSS	Left Ventricle	heart
26	chr1:228327200-228329000	Active TSS	Lung	lung
27	chr1:228327200-228329000	Active TSS	A549	lung
28	chr1:228327200-228329000	Active TSS	HSMMtube	muscle
29	chr1:228327200-228329000	Active TSS	NHLF	lung
30	chr1:228327200-228329000	Active TSS	Osteobl	bone
31	chr1:228327200-228329200	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr1:228327200-228329200	Active TSS	Esophagus	oesophagus
33	chr1:228327200-228329200	Active TSS	Ovary	ovary
34	chr1:228327200-228329200	Active TSS	Psoas Muscle	Psoas
35	chr1:228327200-228329200	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr1:228327200-228329400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:228327200-228329400	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr1:228327200-228329400	Active TSS	NHDF-Ad	bronchial
39	chr1:228327400-228328800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:228327400-228328800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr1:228327400-228328800	Active TSS	Duodenum Mucosa	Duodenum
42	chr1:228327400-228328800	Active TSS	Fetal Brain Female	brain
43	chr1:228327400-228328800	Active TSS	Fetal Intestine Large	intestine
44	chr1:228327400-228328800	Active TSS	Hela-S3	cervix
45	chr1:228327400-228328800	Active TSS	NH-A	brain
46	chr1:228327400-228329000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr1:228327400-228329000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:228327400-228329000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:228327400-228329000	Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr1:228327400-228329000	Active TSS	Aorta	Aorta

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