Variant report

Variant	rs12647095
Chromosome Location	chr4:90033240-90033241
allele	A/C
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	FOXA1	chr4:90033231-90033905	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:90032026-90033501	GM18505	blood:	n/a	n/a
3	BHLHE40	chr4:90032021-90033369	GM12878	blood:	n/a	chr4:90032093-90032109
4	ARID3A	chr4:90032770-90035534	HepG2	liver:	n/a	n/a
5	MYBL2	chr4:90033181-90033902	HepG2	liver:	n/a	n/a
6	RELA	chr4:90031877-90033556	GM10847	blood:	n/a	n/a
7	EP300	chr4:90032219-90033272	GM12878	blood:	n/a	chr4:90032597-90032613
8	MAX	chr4:90031702-90033805	A549	lung:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
9	POLR2A	chr4:90032368-90036875	HepG2	liver:	n/a	n/a
10	CEBPB	chr4:90033137-90033959	MCF-7	breast:	n/a	chr4:90033558-90033567 chr4:90033558-90033567 chr4:90033558-90033567 chr4:90033556-90033569 chr4:90033558-90033567
11	POLR2A	chr4:90031741-90033492	GM19099	blood:	n/a	n/a
12	EP300	chr4:90032221-90033588	K562	blood:	n/a	chr4:90032597-90032613
13	CHD2	chr4:90032261-90033380	K562	blood:	n/a	n/a
14	CEBPB	chr4:90033036-90033954	A549	lung:	n/a	chr4:90033558-90033567 chr4:90033558-90033567 chr4:90033558-90033567 chr4:90033556-90033569 chr4:90033558-90033567
15	FOXA1	chr4:90033178-90033817	HepG2	liver:	n/a	n/a
16	CREB1	chr4:90032077-90033871	HepG2	liver:	n/a	n/a
17	FOS	chr4:90033161-90033809	MCF10A-Er-Src	breast:	n/a	chr4:90033397-90033406
18	CTCF	chr4:90032056-90033299	K562	blood:	n/a	n/a
19	SP1	chr4:90033222-90033862	A549	lung:	n/a	n/a
20	GTF2F1	chr4:90032316-90033736	Hela-S3	cervix:	n/a	n/a
21	CHD1	chr4:90031786-90033305	GM12878	blood:	n/a	n/a
22	CEBPB	chr4:90033222-90033807	A549	lung:	n/a	chr4:90033558-90033567 chr4:90033558-90033567 chr4:90033558-90033567 chr4:90033556-90033569 chr4:90033558-90033567
23	MAZ	chr4:90032333-90033993	HepG2	liver:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
24	CEBPB	chr4:90032375-90033816	Hela-S3	cervix:	n/a	chr4:90033558-90033567 chr4:90033558-90033567 chr4:90033558-90033567 chr4:90033556-90033569 chr4:90033558-90033567
25	POLR2A	chr4:90032187-90033680	GM15510	blood:	n/a	n/a
26	UBTF	chr4:90031882-90033927	K562	blood:	n/a	n/a
27	POLR2A	chr4:90032545-90033803	MCF10A-Er-Src	breast:	n/a	n/a
28	ELK1	chr4:90032318-90033602	Hela-S3	cervix:	n/a	n/a
29	MAX	chr4:90032095-90033273	HCT-116	colon:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
30	MYC	chr4:90031728-90033645	K562	blood:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
31	MXI1	chr4:90031723-90034038	HepG2	liver:	n/a	chr4:90031789-90031804
32	CCNT2	chr4:90031987-90033323	K562	blood:	n/a	chr4:90032568-90032577 chr4:90032597-90032606 chr4:90032633-90032642
33	TEAD4	chr4:90033179-90034004	HepG2	liver:	n/a	n/a
34	FOS	chr4:90033108-90033770	MCF10A-Er-Src	breast:	n/a	chr4:90033397-90033406
35	SIN3AK20	chr4:90033165-90033920	MCF-7	breast:	n/a	n/a
36	TBP	chr4:90032698-90033684	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr4:90033100-90033250	HAc	cerebellar:	n/a	n/a
38	POLR2A	chr4:90031750-90033337	GM12878	blood:	n/a	n/a
39	RCOR1	chr4:90031445-90033946	K562	blood:	n/a	n/a
40	WRNIP1	chr4:90031705-90033370	GM12878	blood:	n/a	n/a
41	MYC	chr4:90033198-90033875	MCF10A-Er-Src	breast:	n/a	n/a
42	JUND	chr4:90031790-90033679	K562	blood:	n/a	chr4:90033397-90033406
43	MAZ	chr4:90031500-90033296	K562	blood:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
44	POLR2A	chr4:90032398-90034599	HepG2	liver:	n/a	n/a
45	POLR2A	chr4:90032629-90036890	K562	blood:	n/a	n/a
46	MAX	chr4:90031994-90033706	HCT-116	colon:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
47	CEBPB	chr4:90033211-90033938	HCT-116	colon:	n/a	chr4:90033558-90033567 chr4:90033558-90033567 chr4:90033558-90033567 chr4:90033556-90033569 chr4:90033558-90033567
48	SIN3A	chr4:90031671-90033679	H1-hESC	embryonic stem cell:	n/a	chr4:90031994-90032003 chr4:90032056-90032070 chr4:90031990-90032004 chr4:90032616-90032627 chr4:90031996-90032004
49	E2F4	chr4:90032394-90033741	MCF10A-Er-Src	breast:	n/a	chr4:90032663-90032672 chr4:90032574-90032586 chr4:90032633-90032642 chr4:90032628-90032638
50	REST	chr4:90031556-90033473	H1-neurons	neurons:	n/a	chr4:90031993-90032003 chr4:90032055-90032069 chr4:90032055-90032075 chr4:90031991-90032005 chr4:90032057-90032067 chr4:90032055-90032075 chr4:90032059-90032072 chr4:90031988-90032001 chr4:90032056-90032074

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:89977166..89979264-chr4:90032025..90033904,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TIGD2-2	chr4:90033218-90033519	ENSG00000271359.1

Variant related genes	Relation type
FAM13A	TF binding region
TIGD2	TF binding region
ENSG00000138640	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10001420	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10433881	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734924	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12645173	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12649875	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13105546	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133608	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138927	0.96[ASN][1000 genomes]
rs1355836	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1355837	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1398937	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1398938	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1398939	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1398941	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1398943	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1513811	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1513812	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1513823	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1533288	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1533289	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1533294	0.96[ASN][1000 genomes]
rs1708659	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1708671	0.85[ASN][1000 genomes]
rs1708672	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1708673	0.81[ASN][1000 genomes]
rs1708683	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1795730	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1795735	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1795737	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1795740	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1828735	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1996139	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2056013	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2102650	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2464511	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2670618	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2670619	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2670620	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2670627	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2670628	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2704580	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2704585	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2704592	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28559811	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2869989	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28718401	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28869547	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2904264	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4325981	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4693219	0.83[AMR][1000 genomes]
rs4693984	0.81[AMR][1000 genomes]
rs4693987	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6532100	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6532113	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823241	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826482	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6834297	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6843986	0.86[ASN][1000 genomes]
rs6845264	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6846010	0.92[ASN][1000 genomes]
rs7657630	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180333	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9307063	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs938265	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs938267	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999793	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9999873	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3437234	chr4:90031454-90034302	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr4:90030800-90033600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr4:90031000-90033400	Active TSS	Pancreas	Pancrea
3	chr4:90031200-90033400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr4:90031400-90033400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
5	chr4:90031400-90033400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr4:90031400-90033600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:90031600-90033400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr4:90031600-90033400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:90031600-90033400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr4:90031600-90033400	Active TSS	Right Atrium	heart
11	chr4:90031600-90033600	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr4:90031600-90033600	Active TSS	Placenta Amnion	Placenta Amnion
13	chr4:90031800-90033400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr4:90031800-90033400	Active TSS	Fetal Brain Male	brain
15	chr4:90031800-90033400	Active TSS	Fetal Heart	heart
16	chr4:90031800-90033400	Active TSS	Psoas Muscle	Psoas
17	chr4:90031800-90033600	Active TSS	Aorta	Aorta
18	chr4:90031800-90033600	Active TSS	Fetal Kidney	kidney
19	chr4:90031800-90033600	Active TSS	Gastric	stomach
20	chr4:90031800-90033800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr4:90032000-90033400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:90032000-90033400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:90032000-90033400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:90032000-90033400	Active TSS	Liver	Liver
25	chr4:90032000-90033400	Active TSS	Ovary	ovary
26	chr4:90032000-90033400	Active TSS	Stomach Mucosa	stomach
27	chr4:90032000-90033400	Active TSS	K562	blood
28	chr4:90032000-90033600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:90032000-90033600	Active TSS	Brain Angular Gyrus	brain
30	chr4:90032000-90033600	Active TSS	Right Ventricle	heart
31	chr4:90032000-90033800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:90032000-90033800	Active TSS	A549	lung
33	chr4:90032000-90034000	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr4:90032200-90033400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:90032200-90033400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:90032200-90033400	Active TSS	Esophagus	oesophagus
37	chr4:90032200-90033400	Active TSS	Lung	lung
38	chr4:90032200-90033400	Active TSS	HSMM	muscle
39	chr4:90032200-90033600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:90032200-90033600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr4:90032200-90033600	Active TSS	Left Ventricle	heart
42	chr4:90032200-90033600	Active TSS	HSMMtube	muscle
43	chr4:90032200-90033600	Active TSS	NHDF-Ad	bronchial
44	chr4:90032200-90033800	Active TSS	GM12878-XiMat	blood
45	chr4:90032200-90033800	Active TSS	NHLF	lung
46	chr4:90032400-90033400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:90032400-90033400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr4:90032400-90033800	Active TSS	Fetal Intestine Large	intestine
49	chr4:90032400-90033800	Active TSS	Stomach Smooth Muscle	stomach
50	chr4:90032400-90034000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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