Variant report

Variant	rs12499164
Chromosome Location	chr4:48272300-48272301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:309)
CpG islands
(count:122)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:309 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr4:48271327-48272545	K562	blood:	n/a	n/a
2	BHLHE40	chr4:48270826-48272646	GM12878	blood:	n/a	chr4:48272386-48272407 chr4:48272391-48272400 chr4:48271167-48271176 chr4:48271162-48271183
3	SIN3AK20	chr4:48272091-48272381	H1-hESC	embryonic stem cell:	n/a	n/a
4	RCOR1	chr4:48272017-48272802	K562	blood:	n/a	n/a
5	POLR2A	chr4:48271912-48272687	GM12892	blood:	n/a	n/a
6	TEAD4	chr4:48271919-48272352	K562	blood:	n/a	n/a
7	PAX5	chr4:48271908-48272554	GM12878	blood:	n/a	chr4:48272422-48272441 chr4:48272084-48272094
8	PML	chr4:48271272-48272558	K562	blood:	n/a	n/a
9	EBF1	chr4:48271914-48272469	GM12878	blood:	n/a	chr4:48272152-48272163
10	MAX	chr4:48271923-48272561	ECC-1	luminal epithelium:	n/a	n/a
11	EGR1	chr4:48271890-48272347	H1-hESC	embryonic stem cell:	n/a	n/a
12	TAF1	chr4:48271383-48272432	ECC-1	luminal epithelium:	n/a	n/a
13	MAFK	chr4:48272040-48273352	Hela-S3	cervix:	n/a	chr4:48273198-48273213
14	CTCF	chr4:48272240-48272390	GM12801	blood:	n/a	n/a
15	ZNF143	chr4:48272028-48272394	H1-hESC	embryonic stem cell:	n/a	n/a
16	TAF1	chr4:48271950-48272375	PFSK-1	brain:	n/a	n/a
17	CTCF	chr4:48272200-48272350	HL-60	blood:	n/a	n/a
18	RELA	chr4:48271745-48272697	GM19099	blood:	n/a	n/a
19	CTCF	chr4:48272200-48272350	GM12873	blood:	n/a	n/a
20	POLR2A	chr4:48271205-48272817	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:48271295-48272388	K562	blood:	n/a	n/a
22	POLR2A	chr4:48271921-48272371	A549	lung:	n/a	n/a
23	GTF2F1	chr4:48271931-48272515	Hela-S3	cervix:	n/a	n/a
24	TBP	chr4:48271947-48272619	GM12878	blood:	n/a	n/a
25	E2F6	chr4:48272193-48272391	K562	blood:	n/a	n/a
26	POLR2A	chr4:48271330-48272331	MCF-7	breast:	n/a	n/a
27	CTCF	chr4:48272220-48272370	NHEK	skin:	n/a	n/a
28	BHLHE40	chr4:48269776-48272702	K562	blood:	n/a	chr4:48272386-48272407 chr4:48272391-48272400 chr4:48271167-48271176 chr4:48271162-48271183
29	CTCF	chr4:48271846-48272496	GM12878	blood:	n/a	chr4:48272167-48272176
30	TCF7L2	chr4:48271150-48272503	HCT-116	colon:	n/a	chr4:48271163-48271172
31	PAX5	chr4:48271477-48272352	GM12892	blood:	n/a	chr4:48272084-48272094
32	MAFK	chr4:48272030-48273395	K562	blood:	n/a	chr4:48273198-48273213
33	BACH1	chr4:48272285-48272805	K562	blood:	n/a	n/a
34	EP300	chr4:48271984-48272537	K562	blood:	n/a	chr4:48272115-48272124
35	RELA	chr4:48271221-48273441	GM19193	blood:	n/a	n/a
36	POLR2A	chr4:48271297-48272377	GM12878	blood:	n/a	n/a
37	POLR2A	chr4:48271148-48272531	GM15510	blood:	n/a	n/a
38	USF1	chr4:48272204-48272588	A549	lung:	n/a	chr4:48272386-48272407 chr4:48272391-48272400 chr4:48272390-48272401
39	UBTF	chr4:48271302-48272505	K562	blood:	n/a	n/a
40	FOXM1	chr4:48271892-48272612	GM12878	blood:	n/a	n/a
41	BCL3	chr4:48271926-48272500	GM12878	blood:	n/a	chr4:48272028-48272041
42	HDAC2	chr4:48271324-48272522	MCF-7	breast:	n/a	n/a
43	KAP1	chr4:48272095-48273922	HEK293	kidney:	n/a	n/a
44	TRIM28	chr4:48271961-48272500	K562	blood:	n/a	n/a
45	STAT3	chr4:48272024-48272372	MCF10A-Er-Src	breast:	n/a	n/a
46	ARID3A	chr4:48271978-48272494	K562	blood:	n/a	n/a
47	POLR2A	chr4:48271343-48272565	K562	blood:	n/a	n/a
48	CTCF	chr4:48272160-48272310	NHEK	skin:	n/a	chr4:48272167-48272176
49	POLR2A	chr4:48271937-48272313	A549	lung:	n/a	n/a
50	CTCF	chr4:48272180-48272330	MCF-7	breast:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:48272297-48272347	NT2-D1	testis:	n/a
2	chr4:48272297-48272347	HRE	kidney:	n/a
3	chr4:48272266-48272316	ovcar-3	ovarian:	n/a
4	chr4:48272266-48272316	BE2_C	brain:	n/a
5	chr4:48272297-48272347	Hela-S3	cervix:	n/a
6	chr4:48272266-48272316	HNPCEpiC	eye:	n/a
7	chr4:48272266-48272316	MCF-7	breast:	n/a
8	chr4:48272266-48272316	SK-N-SH	brain:	n/a
9	chr4:48272297-48272347	MCF-7	breast:	n/a
10	chr4:48272297-48272347	GM12891	blood:	n/a
11	chr4:48272266-48272316	ProgFib	skin:	n/a
12	chr4:48272297-48272347	ProgFib	skin:	n/a
13	chr4:48272266-48272316	HPAEpiC	pulmonary alveolar:	n/a
14	chr4:48272266-48272316	SAEC	small airway:	n/a
15	chr4:48272266-48272316	AG10803	skin:	n/a
16	chr4:48272266-48272316	AG04450	lung:	fetal
17	chr4:48272266-48272316	GM19239	blood:	n/a
18	chr4:48272266-48272316	HCPEpiC	choroid plexus:	n/a
19	chr4:48272266-48272316	A549	lung:	n/a
20	chr4:48272297-48272347	BJ	skin:	n/a
21	chr4:48272297-48272347	HRPEpiC	eye:	n/a
22	chr4:48272297-48272347	NH-A	brain:	n/a
23	chr4:48272297-48272347	ovcar-3	ovarian:	n/a
24	chr4:48272297-48272347	Hepatocyte	liver:	n/a
25	chr4:48272266-48272316	SK-N-MC	brain:	n/a
26	chr4:48272297-48272347	AG04450	lung:	fetal
27	chr4:48272297-48272347	PFSK-1	brain:	n/a
28	chr4:48272266-48272316	SK-N-SH_RA	brain:	n/a
29	chr4:48272266-48272316	Hela-S3	cervix:	n/a
30	chr4:48272297-48272347	HEEpiC	esophagus:	n/a
31	chr4:48272297-48272347	AG10803	skin:	n/a
32	chr4:48272297-48272347	AG09319	gingival:	n/a
33	chr4:48272297-48272347	MCF10A-Er-Src	breast:	n/a
34	chr4:48272266-48272316	RPTEC	kidney:	n/a
35	chr4:48272266-48272316	HL-60	blood:	n/a
36	chr4:48272266-48272316	NH-A	brain:	n/a
37	chr4:48272297-48272347	HCF	heart:	n/a
38	chr4:48272297-48272347	Caco-2	colon:	n/a
39	chr4:48272297-48272347	HPAEpiC	pulmonary alveolar:	n/a
40	chr4:48272297-48272347	GM19239	blood:	n/a
41	chr4:48272266-48272316	HIPEpiC	eye:	n/a
42	chr4:48272266-48272316	HCM	heart:	n/a
43	chr4:48272297-48272347	SK-N-SH_RA	brain:	n/a
44	chr4:48272266-48272316	PFSK-1	brain:	n/a
45	chr4:48272266-48272316	GM06990	blood:	n/a
46	chr4:48272297-48272347	GM12892	blood:	n/a
47	chr4:48272297-48272347	HRCEpiC	kidney:	n/a
48	chr4:48272266-48272316	AG04449	skin:	fetal
49	chr4:48272266-48272316	NHBE	bronchial:	n/a
50	chr4:48272266-48272316	HCT-116	colon:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:48271855..48272497-chr7:75544014..75544536,2	NB4	blood:
2	chr3:156392017..156392697-chr4:48272003..48272899,2	NB4	blood:
3	chr4:48270358..48273390-chr4:48340605..48344777,4	MCF-7	breast:
4	chr4:48270141..48273598-chr4:48341900..48344865,7	K562	blood:
5	chr1:110090966..110091798-chr4:48271404..48272367,2	Hela-S3	cervix:
6	chr16:9185283..9185902-chr4:48271309..48272302,2	Hela-S3	cervix:
7	chr4:48167349..48169980-chr4:48272046..48273556,2	K562	blood:
8	chr4:48269261..48273807-chr4:48342628..48344865,6	K562	blood:

No data

Variant related genes	Relation type
TEC	TF binding region
TEC	CpG island
ENSG00000127948	Chromatin interaction
ENSG00000265020	Chromatin interaction
ENSG00000065135	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000182831	Chromatin interaction
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12510551	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12640519	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12645266	0.91[AMR][1000 genomes]
rs13127675	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1876835	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2055800	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2136502	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2352595	1.00[AMR][1000 genomes]
rs2464503	1.00[AMR][1000 genomes]
rs2704393	0.85[AMR][1000 genomes]
rs2704411	1.00[AMR][1000 genomes]
rs309882	0.83[AMR][1000 genomes]
rs309886	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs309888	0.82[AFR][1000 genomes]
rs309889	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs309893	0.91[AMR][1000 genomes]
rs309894	0.91[AMR][1000 genomes]
rs309895	0.91[AMR][1000 genomes]
rs409176	0.91[AMR][1000 genomes]
rs4095347	0.86[AFR][1000 genomes]
rs419804	0.91[AMR][1000 genomes]
rs4235154	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs436979	0.91[AMR][1000 genomes]
rs4478160	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4695367	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4695368	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6447624	0.91[AMR][1000 genomes]
rs6819233	0.91[AMR][1000 genomes]
rs7661341	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs937952	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]

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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48269800-48272800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:48270000-48272400	Active TSS	Primary T killer memory cells from peripheral blood	blood
3	chr4:48270600-48272400	Active TSS	Right Ventricle	heart
4	chr4:48270600-48272600	Active TSS	NHDF-Ad	bronchial
5	chr4:48270600-48272800	Active TSS	A549	lung
6	chr4:48270600-48272800	Active TSS	NHLF	lung
7	chr4:48270800-48272400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr4:48270800-48272400	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr4:48270800-48272400	Active TSS	Fetal Intestine Large	intestine
10	chr4:48270800-48272400	Active TSS	Fetal Intestine Small	intestine
11	chr4:48270800-48272400	Active TSS	Fetal Kidney	kidney
12	chr4:48270800-48272400	Active TSS	Fetal Lung	lung
13	chr4:48270800-48272400	Active TSS	HSMM	muscle
14	chr4:48270800-48272400	Active TSS	K562	blood
15	chr4:48270800-48272600	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr4:48270800-48272600	Active TSS	HSMMtube	muscle
17	chr4:48270800-48272800	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr4:48270800-48272800	Active TSS	H9 Cell Line	embryonic stem cell
19	chr4:48270800-48272800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:48270800-48272800	Active TSS	Primary T cells from cord blood	blood
21	chr4:48270800-48272800	Active TSS	Rectal Smooth Muscle	rectum
22	chr4:48271000-48272400	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr4:48271000-48272400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:48271000-48272400	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr4:48271000-48272400	Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr4:48271000-48272400	Active TSS	Duodenum Mucosa	Duodenum
27	chr4:48271000-48272400	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr4:48271000-48272400	Active TSS	Hela-S3	cervix
29	chr4:48271000-48272600	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr4:48271000-48272600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:48271000-48272600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr4:48271000-48272600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:48271000-48272600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:48271000-48272600	Active TSS	Liver	Liver
35	chr4:48271000-48272600	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr4:48271000-48272600	Active TSS	Left Ventricle	heart
37	chr4:48271000-48272600	Active TSS	Psoas Muscle	Psoas
38	chr4:48271000-48272600	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr4:48271000-48272600	Bivalent/Poised TSS	HepG2	liver
40	chr4:48271000-48272600	Active TSS	HMEC	breast
41	chr4:48271000-48272800	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr4:48271000-48272800	Active TSS	Colon Smooth Muscle	Colon
43	chr4:48271200-48272400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr4:48271200-48272400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:48271200-48272400	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr4:48271200-48272400	Active TSS	Primary monocytes fromperipheralblood	blood
47	chr4:48271200-48272400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:48271200-48272400	Active TSS	Brain Cingulate Gyrus	brain
49	chr4:48271200-48272400	Active TSS	Brain Hippocampus Middle	brain
50	chr4:48271200-48272400	Active TSS	Esophagus	oesophagus

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