Variant report

Variant	rs4768928
Chromosome Location	chr12:50784356-50784357
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	CEBPB	chr12:50783986-50784560	A549	lung:	n/a	n/a
2	MAFK	chr12:50784036-50784414	IMR90	lung:	n/a	chr12:50784055-50784070
3	JUND	chr12:50783933-50784602	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr12:50783953-50784535	HUVEC	blood vessel:	n/a	n/a
5	MAX	chr12:50784105-50784494	Hela-S3	cervix:	n/a	n/a
6	NR3C1	chr12:50784055-50784470	A549	lung:	n/a	n/a
7	JUND	chr12:50784035-50784470	HepG2	liver:	n/a	n/a
8	NFIC	chr12:50783932-50784651	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr12:50784163-50784480	U87	brain:	n/a	n/a
10	RAD21	chr12:50784065-50784511	Hela-S3	cervix:	n/a	n/a
11	SMARCC1	chr12:50783825-50784514	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:50784239-50784533	Hela-S3	cervix:	n/a	n/a
13	FOSL2	chr12:50784040-50784535	MCF-7	breast:	n/a	n/a
14	POLR2A	chr12:50784040-50784518	SK-N-SH	brain:	n/a	n/a
15	FOSL1	chr12:50783898-50784581	HCT-116	colon:	n/a	n/a
16	TAF1	chr12:50784214-50784548	Hela-S3	cervix:	n/a	n/a
17	TCF12	chr12:50783890-50784741	SK-N-SH	brain:	n/a	n/a
18	REST	chr12:50784130-50784538	Hela-S3	cervix:	n/a	n/a
19	FOSL2	chr12:50783996-50784431	A549	lung:	n/a	n/a
20	STAT3	chr12:50783965-50784512	Hela-S3	cervix:	n/a	chr12:50784293-50784304
21	EP300	chr12:50784053-50784473	Hela-S3	cervix:	n/a	n/a
22	STAT3	chr12:50783871-50784528	MCF10A-Er-Src	breast:	n/a	chr12:50784293-50784304
23	EP300	chr12:50784093-50784491	SK-N-SH_RA	brain:	n/a	n/a
24	E2F4	chr12:50784133-50784380	MCF10A-Er-Src	breast:	n/a	n/a
25	MYC	chr12:50784091-50784490	MCF10A-Er-Src	breast:	n/a	n/a
26	JUND	chr12:50783987-50784530	Hela-S3	cervix:	n/a	n/a
27	CEBPB	chr12:50784045-50784534	Hela-S3	cervix:	n/a	n/a
28	ARID3A	chr12:50784138-50784465	HepG2	liver:	n/a	n/a
29	FOS	chr12:50784018-50784552	MCF10A-Er-Src	breast:	n/a	n/a
30	STAT3	chr12:50783969-50784589	MCF10A-Er-Src	breast:	n/a	chr12:50784293-50784304
31	USF2	chr12:50784139-50784490	Hela-S3	cervix:	n/a	n/a
32	MYC	chr12:50784056-50784490	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr12:50784003-50784553	HUVEC	blood vessel:	n/a	n/a
34	CBX3	chr12:50783928-50784630	HCT-116	colon:	n/a	n/a
35	FOSL2	chr12:50783808-50784597	A549	lung:	n/a	n/a
36	STAT3	chr12:50784005-50784589	MCF10A-Er-Src	breast:	n/a	chr12:50784293-50784304
37	FOS	chr12:50783774-50784542	MCF10A-Er-Src	breast:	n/a	n/a
38	REST	chr12:50784246-50784443	Hela-S3	cervix:	n/a	n/a
39	STAT3	chr12:50783961-50784589	MCF10A-Er-Src	breast:	n/a	chr12:50784293-50784304
40	MYC	chr12:50784267-50784369	HUVEC	blood vessel:	n/a	n/a
41	FOSL2	chr12:50783827-50784647	SK-N-SH	brain:	n/a	n/a
42	FOS	chr12:50784032-50784526	Hela-S3	cervix:	n/a	n/a
43	TCF12	chr12:50783946-50784652	SK-N-SH	brain:	n/a	n/a
44	CEBPB	chr12:50784172-50784494	IMR90	lung:	n/a	n/a
45	TEAD4	chr12:50783991-50784485	HepG2	liver:	n/a	n/a
46	POLR2A	chr12:50784271-50784581	MCF10A-Er-Src	breast:	n/a	n/a
47	FOS	chr12:50783875-50784552	MCF10A-Er-Src	breast:	n/a	n/a
48	NR3C1	chr12:50783931-50784613	A549	lung:	n/a	n/a
49	POLR2A	chr12:50783983-50784541	Hela-S3	cervix:	n/a	n/a
50	RCOR1	chr12:50784049-50784556	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50784065..50785899-chr12:50794151..50795711,2	MCF-7	breast:
2	chr12:50782728..50784449-chr12:50792559..50794993,2	K562	blood:

Variant related genes	Relation type
LARP4	TF binding region
ENSG00000161813	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10506293	0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs10735825	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10747580	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10747581	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783362	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10876030	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876034	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169408	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11169422	0.82[ASN][1000 genomes]
rs11169427	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169440	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11503904	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11610442	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12099511	0.87[ASN][1000 genomes]
rs12307602	0.87[ASN][1000 genomes]
rs12578525	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12824882	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17119774	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs17119778	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17124672	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs17531020	0.95[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs4238104	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4257057	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4298982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4351895	0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4450234	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4768877	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768878	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768879	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768880	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768936	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4768951	0.93[YRI][hapmap]
rs56671180	0.85[ASN][1000 genomes]
rs56989201	0.82[ASN][1000 genomes]
rs57283487	0.81[ASN][1000 genomes]
rs57293958	0.82[ASN][1000 genomes]
rs57578212	0.92[ASN][1000 genomes]
rs57811009	0.86[ASN][1000 genomes]
rs57828015	0.82[ASN][1000 genomes]
rs58500867	0.87[ASN][1000 genomes]
rs58869591	0.91[ASN][1000 genomes]
rs58888905	0.87[ASN][1000 genomes]
rs58916974	0.88[ASN][1000 genomes]
rs59696942	0.83[ASN][1000 genomes]
rs59968707	0.83[ASN][1000 genomes]
rs60010359	0.87[ASN][1000 genomes]
rs60198651	0.82[ASN][1000 genomes]
rs60201334	0.82[ASN][1000 genomes]
rs60242613	0.82[ASN][1000 genomes]
rs60420087	0.86[ASN][1000 genomes]
rs60610745	0.94[ASN][1000 genomes]
rs60743903	0.83[ASN][1000 genomes]
rs61578731	0.83[ASN][1000 genomes]
rs6580736	0.91[YRI][hapmap]
rs6580753	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6580754	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7133488	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7135159	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7138063	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7295610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7295698	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7296212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7299321	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7304017	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7304262	0.81[ASN][1000 genomes]
rs7310094	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7955176	0.96[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7957033	0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7965165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7974480	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7978625	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
2	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv1053667	chr12:50679039-50801752	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1054480	chr12:50691039-50859665	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv1041563	chr12:50705715-50861699	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1049665	chr12:50705715-50871542	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv899076	chr12:50770291-50869589	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50780800-50786200	Enhancers	Placenta	Placenta
2	chr12:50781800-50794000	Weak transcription	Fetal Kidney	kidney
3	chr12:50782000-50790400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:50782000-50794000	Weak transcription	Fetal Heart	heart
5	chr12:50782400-50784600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:50782400-50790400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:50782800-50784800	Enhancers	HepG2	liver
8	chr12:50782800-50794200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:50783400-50784400	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr12:50783400-50784800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:50783400-50784800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:50783400-50784800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:50783400-50784800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:50783400-50784800	Enhancers	Osteobl	bone
15	chr12:50783400-50785000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:50783400-50785000	Enhancers	HMEC	breast
17	chr12:50783400-50785000	Enhancers	NHDF-Ad	bronchial
18	chr12:50783400-50785800	Enhancers	Hela-S3	cervix
19	chr12:50783600-50784600	Enhancers	Fetal Intestine Small	intestine
20	chr12:50783600-50784800	Enhancers	Fetal Intestine Large	intestine
21	chr12:50783600-50784800	Enhancers	HSMM	muscle
22	chr12:50783600-50784800	Enhancers	NHEK	skin
23	chr12:50783600-50784800	Enhancers	NHLF	lung
24	chr12:50783600-50785000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:50783800-50784600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:50783800-50784600	Enhancers	Small Intestine	intestine
27	chr12:50783800-50784800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:50783800-50785000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:50783800-50785600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:50784200-50784400	Enhancers	Muscle Satellite Cultured Cells	--
31	chr12:50784200-50784400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:50784200-50784400	Enhancers	Gastric	stomach
33	chr12:50784200-50784400	Enhancers	HUVEC	blood vessel
34	chr12:50784200-50784600	Flanking Active TSS	A549	lung
35	chr12:50784200-50784800	Enhancers	HSMMtube	muscle
36	chr12:50784200-50784800	Enhancers	NH-A	brain

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