Variant report

Variant	rs4653908
Chromosome Location	chr1:228327999-228328000
allele	C/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	NFIC	chr1:228327297-228328069	GM12878	blood:	n/a	n/a
2	GTF2F1	chr1:228327475-228328229	K562	blood:	n/a	n/a
3	PAX5	chr1:228327501-228328294	GM12892	blood:	n/a	n/a
4	GABPA	chr1:228327467-228328239	HepG2	liver:	n/a	chr1:228327695-228327704
5	HEY1	chr1:228327769-228328706	K562	blood:	n/a	chr1:228327905-228327920
6	POLR2A	chr1:228327199-228329184	GM12878	blood:	n/a	n/a
7	SP1	chr1:228327541-228328159	H1-hESC	embryonic stem cell:	n/a	chr1:228327694-228327706 chr1:228327696-228327705 chr1:228327875-228327887 chr1:228327901-228327911 chr1:228327876-228327885 chr1:228327900-228327912 chr1:228327877-228327886 chr1:228327901-228327910 chr1:228327694-228327706 chr1:228327835-228327844 chr1:228327695-228327705 chr1:228327831-228327845 chr1:228327902-228327911 chr1:228327695-228327705 chr1:228327834-228327846 chr1:228327836-228327845 chr1:228327695-228327704 chr1:228327877-228327886
8	POLR2A	chr1:228327252-228328311	HL-60	blood:	n/a	n/a
9	CHD2	chr1:228327410-228328229	H1-hESC	embryonic stem cell:	n/a	n/a
10	TCF12	chr1:228327415-228328530	ECC-1	luminal epithelium:	n/a	chr1:228328358-228328365 chr1:228328380-228328390
11	POLR2A	chr1:228327107-228328712	Raji	blood:	n/a	n/a
12	TBL1XR1	chr1:228327341-228328445	GM12878	blood:	n/a	n/a
13	TCF3	chr1:228327579-228328345	GM12878	blood:	n/a	n/a
14	YY1	chr1:228327091-228328654	K562	blood:	n/a	chr1:228328107-228328118 chr1:228328361-228328375 chr1:228327692-228327706 chr1:228327701-228327712 chr1:228328109-228328123 chr1:228327698-228327712
15	CEBPB	chr1:228327524-228328000	HepG2	liver:	n/a	n/a
16	SIN3AK20	chr1:228327202-228328730	MCF-7	breast:	n/a	n/a
17	EGR1	chr1:228327460-228328235	MCF-7	breast:	n/a	chr1:228327977-228327991 chr1:228327941-228327955 chr1:228327593-228327606 chr1:228327691-228327705 chr1:228327835-228327845 chr1:228327695-228327705
18	ZNF143	chr1:228327479-228328096	K562	blood:	n/a	n/a
19	TAF1	chr1:228327500-228328390	HepG2	liver:	n/a	n/a
20	TCF7L2	chr1:228327352-228328115	Hela-S3	cervix:	n/a	chr1:228327627-228327641
21	POLR2A	chr1:228327845-228328552	Hela-S3	cervix:	n/a	n/a
22	CTCF	chr1:228327688-228328002	GM10266	blood:	n/a	chr1:228327829-228327842
23	ARID3A	chr1:228327736-228328143	HepG2	liver:	n/a	n/a
24	SMARCB1	chr1:228327329-228328854	Hela-S3	cervix:	n/a	n/a
25	HEY1	chr1:228327285-228328293	HepG2	liver:	n/a	chr1:228327905-228327920 chr1:228327638-228327653
26	TCF7L2	chr1:228327259-228328174	HCT-116	colon:	n/a	chr1:228327627-228327641
27	KAP1	chr1:228327352-228328130	U2OS	brain:	n/a	n/a
28	EGR1	chr1:228327246-228328434	HCT-116	colon:	n/a	chr1:228327977-228327991 chr1:228328263-228328273 chr1:228327941-228327955 chr1:228327593-228327606 chr1:228327691-228327705 chr1:228327835-228327845 chr1:228327695-228327705
29	POLR2A	chr1:228327150-228328561	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr1:228327882-228328234	GM12891	blood:	n/a	n/a
31	UBTF	chr1:228327292-228329537	K562	blood:	n/a	n/a
32	POLR2A	chr1:228327494-228328294	HepG2	liver:	n/a	n/a
33	ATF2	chr1:228327336-228328088	H1-hESC	embryonic stem cell:	n/a	chr1:228327964-228327978
34	SIN3A	chr1:228327334-228328530	GM12878	blood:	n/a	chr1:228328283-228328296
35	SIN3AK20	chr1:228327332-228328479	SK-N-SH	brain:	n/a	n/a
36	EP300	chr1:228327275-228328440	K562	blood:	n/a	n/a
37	ARID3A	chr1:228327355-228328049	K562	blood:	n/a	n/a
38	SIX5	chr1:228327819-228328088	A549	lung:	n/a	n/a
39	TAF1	chr1:228327759-228328427	SK-N-SH	brain:	n/a	n/a
40	PBX3	chr1:228327331-228328225	A549	lung:	n/a	n/a
41	NRF1	chr1:228327377-228328172	GM12878	blood:	n/a	chr1:228327695-228327704
42	MAX	chr1:228327367-228328246	A549	lung:	n/a	chr1:228327695-228327705
43	TBP	chr1:228327282-228328074	GM12878	blood:	n/a	n/a
44	JUND	chr1:228327859-228328063	H1-hESC	embryonic stem cell:	n/a	n/a
45	TAF1	chr1:228327385-228328191	GM12878	blood:	n/a	n/a
46	ELF1	chr1:228327468-228328152	A549	lung:	n/a	chr1:228327699-228327711 chr1:228328106-228328115
47	EP300	chr1:228327774-228328220	HepG2	liver:	n/a	n/a
48	IRF1	chr1:228327293-228328481	K562	blood:	n/a	chr1:228327834-228327848 chr1:228327875-228327889 chr1:228327694-228327708 chr1:228328263-228328277
49	POLR2A	chr1:228327787-228328641	K562	blood:	n/a	n/a
50	TAF1	chr1:228327794-228328230	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228327365..228329534-chr1:228645028..228646794,2	MCF-7	breast:
2	chr1:228327603..228328346-chr16:2204822..2205763,2	Hela-S3	cervix:
3	chr1:228267667..228275106-chr1:228326600..228331394,10	K562	blood:
4	chr1:228269915..228273320-chr1:228326449..228329096,4	K562	blood:
5	chr1:228293945..228298846-chr1:228325398..228330582,13	K562	blood:
6	chr1:228290240..228294197-chr1:228325970..228329742,3	MCF-7	breast:
7	chr1:228269306..228272326-chr1:228326148..228329488,5	MCF-7	breast:
8	chr1:228294222..228297212-chr1:228327852..228330069,2	MCF-7	breast:
9	chr1:228319215..228325156-chr1:228326279..228328957,6	K562	blood:
10	chr1:228288649..228293430-chr1:228325997..228329591,7	K562	blood:
11	chr1:228327962..228328503-chr14:76126771..76127749,2	Hela-S3	cervix:
12	chr1:228327593..228329181-chr1:228644179..228646860,2	MCF-7	breast:
13	chr1:228327311..228328278-chr1:228353352..228353936,3	K562	blood:
14	chr1:228326695..228329093-chr1:228572036..228574543,2	K562	blood:
15	chr1:228284520..228292111-chr1:228324853..228335412,14	K562	blood:
16	chr1:228286712..228292079-chr1:228327501..228330420,5	MCF-7	breast:
17	chr1:228296521..228297564-chr1:228327615..228328500,3	Hela-S3	cervix:
18	chr1:228327198..228328051-chr1:228353308..228354013,3	MCF-7	breast:
19	chr1:228294705..228298588-chr1:228325821..228329680,6	MCF-7	breast:
20	chr1:228327693..228328321-chr6:146055580..146056537,2	Hela-S3	cervix:
21	chr1:228327795..228330213-chr1:228593794..228595426,3	K562	blood:
22	chr1:228326053..228331395-chr1:228462710..228467617,6	K562	blood:
23	chr1:228326723..228329419-chr1:228644101..228647035,3	K562	blood:
24	chr1:228326283..228328223-chr1:228644101..228647229,3	K562	blood:
25	chr1:228269794..228271921-chr1:228327972..228330804,3	MCF-7	breast:
26	chr1:228293945..228298682-chr1:228326047..228331152,9	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GJC2-2	chr1:228327980-228328064	NONHSAT009981

Variant related genes	Relation type
GUK1	TF binding region
ENSG00000227625	Chromatin interaction
ENSG00000264944	Chromatin interaction
ENSG00000131653	Chromatin interaction
ENSG00000260260	Chromatin interaction
ENSG00000119685	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000206630	Chromatin interaction
ENSG00000112425	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000270104	Chromatin interaction
ENSG00000269934	Chromatin interaction
ENSG00000154358	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000133935	Chromatin interaction
ENSG00000154370	Chromatin interaction
ENSG00000162910	Chromatin interaction
ENSG00000231563	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10127705	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10495278	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10495279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916266	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1094602	0.96[EUR][1000 genomes]
rs1094603	0.96[EUR][1000 genomes]
rs11577976	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11580599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11581169	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11582265	0.83[AFR][1000 genomes]
rs11582369	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11586055	0.80[EUR][1000 genomes]
rs12034268	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12039801	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12048010	0.83[AFR][1000 genomes]
rs1771486	0.88[EUR][1000 genomes]
rs1803695	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28587961	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34687764	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3768330	0.83[AFR][1000 genomes]
rs3795773	0.96[EUR][1000 genomes]
rs3795774	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41303083	0.96[EUR][1000 genomes]
rs4653906	0.86[EUR][1000 genomes]
rs4653909	0.86[EUR][1000 genomes]
rs4653914	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57146523	0.83[AFR][1000 genomes]
rs57657087	0.83[AFR][1000 genomes]
rs61501937	0.80[EUR][1000 genomes]
rs61825156	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61825157	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61825159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61827462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6663726	0.86[EUR][1000 genomes]
rs6668719	0.86[EUR][1000 genomes]
rs7530253	0.96[EUR][1000 genomes]
rs7537552	0.86[EUR][1000 genomes]
rs882451	0.83[AFR][1000 genomes]
rs9287011	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9970544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][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	chr1:228327000-228328000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:228327000-228328000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:228327000-228328400	Active TSS	Brain Cingulate Gyrus	brain
4	chr1:228327000-228328400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr1:228327000-228328600	Active TSS	Brain Anterior Caudate	brain
6	chr1:228327000-228328600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:228327000-228328600	Active TSS	Colonic Mucosa	Colon
8	chr1:228327000-228328600	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr1:228327000-228328600	Active TSS	K562	blood
10	chr1:228327000-228328800	Active TSS	H1 Cell Line	embryonic stem cell
11	chr1:228327000-228328800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:228327000-228328800	Active TSS	Brain Angular Gyrus	brain
13	chr1:228327000-228329000	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr1:228327000-228329000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:228327000-228329200	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr1:228327000-228329200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:228327000-228329400	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr1:228327000-228329400	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr1:228327200-228328200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr1:228327200-228328200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
21	chr1:228327200-228328400	Active TSS	Stomach Smooth Muscle	stomach
22	chr1:228327200-228328600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:228327200-228328600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:228327200-228328600	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr1:228327200-228328600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:228327200-228328600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:228327200-228328600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:228327200-228328600	Active TSS	Brain Substantia Nigra	brain
29	chr1:228327200-228328600	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr1:228327200-228328600	Active TSS	Fetal Lung	lung
31	chr1:228327200-228328600	Active TSS	Pancreas	Pancrea
32	chr1:228327200-228328600	Active TSS	Placenta Amnion	Placenta Amnion
33	chr1:228327200-228328600	Active TSS	Rectal Smooth Muscle	rectum
34	chr1:228327200-228328600	Active TSS	HUVEC	blood vessel
35	chr1:228327200-228328800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr1:228327200-228328800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:228327200-228328800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:228327200-228328800	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr1:228327200-228328800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:228327200-228328800	Active TSS	Brain Hippocampus Middle	brain
41	chr1:228327200-228328800	Active TSS	Colon Smooth Muscle	Colon
42	chr1:228327200-228328800	Active TSS	Right Ventricle	heart
43	chr1:228327200-228328800	Active TSS	Stomach Mucosa	stomach
44	chr1:228327200-228329000	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr1:228327200-228329000	Active TSS	H9 Cell Line	embryonic stem cell
46	chr1:228327200-228329000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:228327200-228329000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:228327200-228329000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:228327200-228329000	Active TSS	Fetal Kidney	kidney
50	chr1:228327200-228329000	Active TSS	Left Ventricle	heart

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