Variant report

Variant	rs12757325
Chromosome Location	chr1:94081024-94081025
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	TCF12	chr1:94080886-94081756	A549	lung:	n/a	chr1:94081221-94081228
2	RXRA	chr1:94080470-94081771	SK-N-SH	brain:	n/a	chr1:94081362-94081384 chr1:94081271-94081284 chr1:94081330-94081339 chr1:94081270-94081277 chr1:94081271-94081284 chr1:94081271-94081284 chr1:94080827-94080843
3	MAFK	chr1:94080693-94081492	HepG2	liver:	n/a	chr1:94081331-94081340 chr1:94081329-94081344 chr1:94081330-94081340
4	CTCF	chr1:94080940-94081090	GM12874	blood:	n/a	n/a
5	JUND	chr1:94079971-94081869	SK-N-SH	brain:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339 chr1:94081328-94081339
6	NFIC	chr1:94080425-94081829	SK-N-SH	brain:	n/a	chr1:94081232-94081260
7	FOS	chr1:94080766-94081882	MCF10A-Er-Src	breast:	n/a	chr1:94081328-94081340 chr1:94081328-94081339 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
8	TEAD4	chr1:94080426-94081863	SK-N-SH	brain:	n/a	chr1:94080668-94080677
9	MAX	chr1:94080209-94081732	A549	lung:	n/a	chr1:94081330-94081339 chr1:94081329-94081338
10	EBF1	chr1:94080732-94081538	GM12878	blood:	n/a	n/a
11	EGR1	chr1:94080830-94081078	K562	blood:	n/a	chr1:94080914-94080923 chr1:94080913-94080922 chr1:94080911-94080925 chr1:94080912-94080925 chr1:94080913-94080924 chr1:94080911-94080926 chr1:94080913-94080923 chr1:94080912-94080925 chr1:94080909-94080923 chr1:94080913-94080924 chr1:94080913-94080923
12	SREBP1	chr1:94080401-94082190	GM12878	blood:	n/a	n/a
13	RUNX3	chr1:94080681-94081906	GM12878	blood:	n/a	n/a
14	HNF4A	chr1:94080649-94081033	HepG2	liver:	n/a	chr1:94080829-94080841 chr1:94080828-94080841 chr1:94080833-94080841 chr1:94080826-94080844 chr1:94080828-94080842 chr1:94080827-94080842 chr1:94080827-94080842 chr1:94080829-94080841
15	FOSL2	chr1:94080393-94081846	SK-N-SH	brain:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
16	FOS	chr1:94080138-94081878	MCF10A-Er-Src	breast:	n/a	chr1:94081328-94081340 chr1:94081328-94081339 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
17	PBX3	chr1:94080587-94081029	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr1:94080678-94081737	GM12892	blood:	n/a	n/a
19	MXI1	chr1:94078695-94084544	SK-N-SH	brain:	n/a	chr1:94082665-94082680
20	CTCF	chr1:94080911-94081050	GM19239	blood:	n/a	n/a
21	FOSL2	chr1:94080585-94081635	HepG2	liver:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
22	EGR1	chr1:94080790-94081067	K562	blood:	n/a	chr1:94080914-94080923 chr1:94080913-94080922 chr1:94080911-94080925 chr1:94080912-94080925 chr1:94080913-94080924 chr1:94080911-94080926 chr1:94080913-94080923 chr1:94080912-94080925 chr1:94080909-94080923 chr1:94080913-94080924 chr1:94080913-94080923
23	MAX	chr1:94080525-94081620	HepG2	liver:	n/a	chr1:94081330-94081339 chr1:94081329-94081338
24	FOSL2	chr1:94080591-94081564	HepG2	liver:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
25	TEAD4	chr1:94080503-94081536	HepG2	liver:	n/a	chr1:94080668-94080677
26	STAT5A	chr1:94080943-94081791	GM12878	blood:	n/a	chr1:94081330-94081339 chr1:94081329-94081338 chr1:94081010-94081017 chr1:94081025-94081033
27	BCLAF1	chr1:94080690-94081833	GM12878	blood:	n/a	chr1:94081329-94081338 chr1:94081330-94081339
28	MBD4	chr1:94080689-94081463	HepG2	liver:	n/a	n/a
29	CEBPB	chr1:94080197-94081284	HepG2	liver:	n/a	n/a
30	FOXA1	chr1:94080658-94081137	HepG2	liver:	n/a	n/a
31	MBD4	chr1:94080691-94081485	HepG2	liver:	n/a	n/a
32	JUND	chr1:94080456-94081813	SK-N-SH	brain:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339 chr1:94081328-94081339
33	HNF4A	chr1:94080634-94081037	HepG2	liver:	n/a	chr1:94080829-94080841 chr1:94080828-94080841 chr1:94080833-94080841 chr1:94080826-94080844 chr1:94080828-94080842 chr1:94080827-94080842 chr1:94080827-94080842 chr1:94080829-94080841
34	TBL1XR1	chr1:94080814-94082104	GM12878	blood:	n/a	n/a
35	BATF	chr1:94080801-94081729	GM12878	blood:	n/a	chr1:94081331-94081341
36	NFIC	chr1:94080503-94081587	HepG2	liver:	n/a	chr1:94081232-94081260
37	RELA	chr1:94080860-94081774	GM19193	blood:	n/a	n/a
38	FOXA1	chr1:94080820-94081047	T-47D	breast:	n/a	n/a
39	CTCF	chr1:94080907-94081078	GM12892	blood:	n/a	n/a
40	POU2F2	chr1:94080745-94081745	GM12891	blood:	n/a	chr1:94081604-94081618 chr1:94081590-94081600 chr1:94081585-94081599 chr1:94081590-94081600 chr1:94081588-94081599 chr1:94081585-94081603 chr1:94081607-94081617 chr1:94081590-94081599 chr1:94081587-94081601 chr1:94081587-94081602 chr1:94081590-94081598 chr1:94081589-94081599 chr1:94081583-94081604 chr1:94081591-94081598 chr1:94081583-94081605 chr1:94081589-94081601
41	EP300	chr1:94080647-94081510	HepG2	liver:	n/a	chr1:94081330-94081339
42	POLR2A	chr1:94080834-94081184	MCF10A-Er-Src	breast:	n/a	n/a
43	MAX	chr1:94080693-94081351	HepG2	liver:	n/a	chr1:94081330-94081339 chr1:94081329-94081338
44	POLR2A	chr1:94080819-94081581	Hela-S3	cervix:	n/a	n/a
45	EGR1	chr1:94080794-94081034	GM12878	blood:	n/a	chr1:94080914-94080923 chr1:94080913-94080922 chr1:94080911-94080925 chr1:94080912-94080925 chr1:94080913-94080924 chr1:94080911-94080926 chr1:94080913-94080923 chr1:94080912-94080925 chr1:94080909-94080923 chr1:94080913-94080924 chr1:94080913-94080923
46	TCF3	chr1:94080838-94081167	GM12878	blood:	n/a	n/a
47	ARID3A	chr1:94080225-94081425	HepG2	liver:	n/a	n/a
48	EP300	chr1:94080733-94081862	GM12878	blood:	n/a	chr1:94081330-94081339
49	MAFF	chr1:94080751-94081482	HepG2	liver:	n/a	chr1:94081328-94081346
50	PAX5	chr1:94080733-94081750	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:94048472..94052407-chr1:94077212..94082015,4	MCF-7	breast:
2	chr1:94074700..94077458-chr1:94080437..94082607,3	K562	blood:
3	chr1:94079843..94082142-chr1:94311555..94313576,2	K562	blood:
4	chr1:94080816..94083593-chr1:94090826..94092537,2	K562	blood:

Variant related genes	Relation type
BCAR3	TF binding region
ENSG00000211575	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11576435	1.00[ASN][1000 genomes]
rs11577352	1.00[ASN][1000 genomes]
rs11579004	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579685	1.00[ASN][1000 genomes]
rs11580965	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11588860	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066343	1.00[ASN][1000 genomes]
rs12073093	1.00[ASN][1000 genomes]
rs12090736	1.00[ASN][1000 genomes]
rs12732557	1.00[ASN][1000 genomes]
rs12739747	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12740779	1.00[ASN][1000 genomes]
rs12744941	1.00[ASN][1000 genomes]
rs12760092	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110063	1.00[ASN][1000 genomes]
rs17110101	1.00[ASN][1000 genomes]
rs17110111	1.00[ASN][1000 genomes]
rs17110179	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17110225	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17110370	1.00[ASN][1000 genomes]
rs1877603	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1877604	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1891138	1.00[ASN][1000 genomes]
rs236343	0.80[EUR][1000 genomes]
rs2818163	1.00[ASN][1000 genomes]
rs34183660	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34423897	1.00[ASN][1000 genomes]
rs34663884	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34666525	1.00[ASN][1000 genomes]
rs34726063	1.00[ASN][1000 genomes]
rs35126293	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35691338	1.00[ASN][1000 genomes]
rs35896714	1.00[ASN][1000 genomes]
rs35972761	1.00[ASN][1000 genomes]
rs36115605	1.00[ASN][1000 genomes]
rs3950119	1.00[ASN][1000 genomes]
rs59996315	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61780979	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61780999	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6660968	1.00[ASN][1000 genomes]
rs6666778	1.00[ASN][1000 genomes]
rs6677770	1.00[ASN][1000 genomes]
rs6679609	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683296	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66966060	1.00[ASN][1000 genomes]
rs67043929	1.00[ASN][1000 genomes]
rs67300695	1.00[ASN][1000 genomes]
rs67354439	1.00[ASN][1000 genomes]
rs67511232	1.00[ASN][1000 genomes]
rs71652539	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72721041	1.00[ASN][1000 genomes]
rs7511890	1.00[ASN][1000 genomes]
rs7525880	1.00[ASN][1000 genomes]
rs7531106	1.00[ASN][1000 genomes]
rs7543098	1.00[ASN][1000 genomes]
rs7543763	1.00[ASN][1000 genomes]
rs7553185	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555302	1.00[ASN][1000 genomes]
rs761802	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94057600-94106400	Weak transcription	Primary B cells from cord blood	blood
2	chr1:94075800-94081400	Strong transcription	Hela-S3	cervix
3	chr1:94077200-94099000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:94077600-94081200	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr1:94077600-94084200	Enhancers	Fetal Brain Male	brain
6	chr1:94078400-94084200	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr1:94078600-94081400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:94078600-94084400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:94078800-94084200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr1:94078800-94084200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr1:94079000-94081400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:94079000-94084000	Enhancers	Brain Substantia Nigra	brain
13	chr1:94079200-94081200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr1:94079200-94081200	Transcr. at gene 5' and 3'	HSMM	muscle
15	chr1:94079200-94081800	Enhancers	Placenta Amnion	Placenta Amnion
16	chr1:94079200-94082800	Enhancers	Duodenum Mucosa	Duodenum
17	chr1:94079200-94084000	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:94079200-94084000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:94079200-94084200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:94079400-94081600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:94079400-94083400	Enhancers	Esophagus	oesophagus
22	chr1:94079400-94084000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:94079400-94084200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:94079400-94084800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:94079400-94086800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:94079400-94088600	Enhancers	Fetal Intestine Large	intestine
27	chr1:94079600-94081400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:94079600-94081600	Enhancers	Colonic Mucosa	Colon
29	chr1:94079600-94082200	Enhancers	Brain Germinal Matrix	brain
30	chr1:94079600-94082600	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr1:94079600-94084200	Enhancers	Fetal Brain Female	brain
32	chr1:94079600-94088000	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr1:94079600-94089400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:94079800-94081200	Enhancers	Aorta	Aorta
35	chr1:94079800-94081400	Enhancers	Lung	lung
36	chr1:94079800-94081400	Enhancers	Right Ventricle	heart
37	chr1:94079800-94081400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr1:94079800-94081800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr1:94079800-94082400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:94079800-94082800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:94079800-94082800	Enhancers	Liver	Liver
42	chr1:94079800-94084000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:94079800-94084000	Enhancers	Fetal Muscle Trunk	muscle
44	chr1:94079800-94084000	Enhancers	Left Ventricle	heart
45	chr1:94079800-94084200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:94079800-94084200	Enhancers	Placenta	Placenta
47	chr1:94079800-94084600	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr1:94079800-94090000	Enhancers	Stomach Mucosa	stomach
49	chr1:94080000-94081200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:94080000-94081400	Enhancers	Fetal Thymus	thymus

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