Variant report

Variant	rs12500187
Chromosome Location	chr4:48273152-48273153
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr4:48272506-48273396	HepG2	liver:	n/a	n/a
2	MAFK	chr4:48272040-48273352	Hela-S3	cervix:	n/a	chr4:48273198-48273213
3	POLR2A	chr4:48272965-48273325	GM12891	blood:	n/a	n/a
4	IRF4	chr4:48273005-48273546	GM12878	blood:	n/a	n/a
5	YY1	chr4:48273040-48273357	GM12892	blood:	n/a	n/a
6	MAFK	chr4:48272030-48273395	K562	blood:	n/a	chr4:48273198-48273213
7	RELA	chr4:48271221-48273441	GM19193	blood:	n/a	n/a
8	KAP1	chr4:48272095-48273922	HEK293	kidney:	n/a	n/a
9	NFIC	chr4:48273101-48273791	GM12878	blood:	n/a	n/a
10	MTA3	chr4:48271915-48273593	GM12878	blood:	n/a	n/a
11	CEBPD	chr4:48272801-48273345	K562	blood:	n/a	n/a
12	BCLAF1	chr4:48272931-48273514	GM12878	blood:	n/a	n/a
13	RUNX3	chr4:48272857-48273579	GM12878	blood:	n/a	n/a
14	POLR2A	chr4:48273040-48273377	GM12878	blood:	n/a	n/a
15	BHLHE40	chr4:48273012-48273470	GM12878	blood:	n/a	n/a
16	RELA	chr4:48271497-48273498	GM10847	blood:	n/a	n/a
17	FOXM1	chr4:48272782-48273566	GM12878	blood:	n/a	n/a
18	ATF1	chr4:48272999-48273508	K562	blood:	n/a	n/a
19	POLR2A	chr4:48271168-48273485	GM12878	blood:	n/a	n/a
20	RCOR1	chr4:48273100-48273421	GM12878	blood:	n/a	n/a
21	TAL1	chr4:48273035-48273262	K562	blood:	n/a	n/a
22	TBL1XR1	chr4:48272743-48273252	K562	blood:	n/a	n/a
23	MAFK	chr4:48272498-48273409	HepG2	liver:	n/a	chr4:48273198-48273213
24	RUNX3	chr4:48272977-48273400	GM12878	blood:	n/a	n/a
25	PML	chr4:48271181-48273650	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:48271182-48273421	GM19099	blood:	n/a	n/a
27	MAFF	chr4:48272328-48273546	K562	blood:	n/a	n/a
28	RCOR1	chr4:48272960-48273317	K562	blood:	n/a	n/a
29	RELA	chr4:48272007-48273547	GM18951	blood:	n/a	n/a
30	MAFK	chr4:48271899-48274278	GM12878	blood:	n/a	chr4:48273198-48273213
31	POLR2A	chr4:48272805-48273450	GM12891	blood:	n/a	n/a
32	RELA	chr4:48271439-48273483	GM15510	blood:	n/a	n/a
33	POLR2A	chr4:48272866-48273360	GM12891	blood:	n/a	n/a
34	MAFK	chr4:48272452-48273396	HepG2	liver:	n/a	chr4:48273198-48273213
35	YY1	chr4:48273046-48273506	GM12891	blood:	n/a	n/a
36	MAFK	chr4:48272406-48273390	IMR90	lung:	n/a	chr4:48273198-48273213
37	YY1	chr4:48273024-48273313	GM12878	blood:	n/a	n/a
38	EP300	chr4:48273047-48273430	GM12878	blood:	n/a	n/a
39	POLR2A	chr4:48272962-48273525	GM12891	blood:	n/a	n/a
40	EP300	chr4:48273052-48273522	GM12878	blood:	n/a	n/a
41	POLR2A	chr4:48270681-48274063	GM12891	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:48270358..48273390-chr4:48340605..48344777,4	MCF-7	breast:
2	chr4:48270141..48273598-chr4:48341900..48344865,7	K562	blood:
3	chr4:48167349..48169980-chr4:48272046..48273556,2	K562	blood:
4	chr4:48272391..48273974-chr4:48279554..48281442,2	MCF-7	breast:
5	chr4:48269261..48273807-chr4:48342628..48344865,6	K562	blood:

No data

Variant related genes	Relation type
TEC	TF binding region
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10454242	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs12504870	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes]
rs12507853	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes]
rs13114469	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13125176	0.80[AFR][1000 genomes]
rs1355218	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs17574806	0.84[AFR][1000 genomes]
rs17574819	1.00[JPT][hapmap];0.84[AFR][1000 genomes]
rs17574847	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes]
rs2352597	0.84[AFR][1000 genomes]
rs2457412	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2664030	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2704391	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs34712902	0.84[AFR][1000 genomes]
rs35602964	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694891	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6814786	0.88[AMR][1000 genomes]
rs7669018	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs9996158	0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482316	chr4:48151953-48338746	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2763359	chr4:48189710-48290233	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
4	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv461357	chr4:48248258-48274152	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	nsv594119	chr4:48248258-48274152	Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
8	nsv470032	chr4:48251915-48312389	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv461358	chr4:48251916-48274152	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
10	nsv594120	chr4:48251916-48274152	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48271600-48273200	Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr4:48272000-48273200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr4:48272200-48273200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:48272200-48273400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr4:48272400-48273400	Flanking Active TSS	K562	blood
6	chr4:48272400-48274600	Weak transcription	Pancreas	Pancrea
7	chr4:48272600-48273200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr4:48272600-48273200	Enhancers	Primary B cells from peripheral blood	blood
9	chr4:48272600-48273200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:48272600-48273200	Enhancers	Fetal Intestine Large	intestine
11	chr4:48272600-48273200	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr4:48272600-48273400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr4:48272600-48273600	Enhancers	Fetal Heart	heart
14	chr4:48272600-48274000	Flanking Active TSS	GM12878-XiMat	blood
15	chr4:48272600-48276600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:48272800-48273200	Enhancers	Primary B cells from cord blood	blood
17	chr4:48272800-48273200	Enhancers	Duodenum Mucosa	Duodenum
18	chr4:48272800-48273200	Active TSS	Thymus	Thymus
19	chr4:48272800-48273400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr4:48272800-48273400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr4:48272800-48273800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:48272800-48275200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr4:48272800-48277200	Weak transcription	Fetal Lung	lung
24	chr4:48273000-48273200	Enhancers	Primary T cells from cord blood	blood
25	chr4:48273000-48273800	Enhancers	Primary hematopoietic stem cells	blood
26	chr4:48273000-48274200	Enhancers	Fetal Thymus	thymus

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