Variant report

Variant	rs62311478
Chromosome Location	chr4:48272501-48272502
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	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	RCOR1	chr4:48272017-48272802	K562	blood:	n/a	n/a
4	POLR2A	chr4:48271912-48272687	GM12892	blood:	n/a	n/a
5	PAX5	chr4:48271908-48272554	GM12878	blood:	n/a	chr4:48272422-48272441 chr4:48272084-48272094
6	PML	chr4:48271272-48272558	K562	blood:	n/a	n/a
7	MAX	chr4:48271923-48272561	ECC-1	luminal epithelium:	n/a	n/a
8	MAFK	chr4:48272040-48273352	Hela-S3	cervix:	n/a	chr4:48273198-48273213
9	RELA	chr4:48271745-48272697	GM19099	blood:	n/a	n/a
10	POLR2A	chr4:48271205-48272817	GM12878	blood:	n/a	n/a
11	GTF2F1	chr4:48271931-48272515	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr4:48272420-48272570	HVMF	connective:	n/a	n/a
13	TBP	chr4:48271947-48272619	GM12878	blood:	n/a	n/a
14	BHLHE40	chr4:48269776-48272702	K562	blood:	n/a	chr4:48272386-48272407 chr4:48272391-48272400 chr4:48271167-48271176 chr4:48271162-48271183
15	TCF7L2	chr4:48271150-48272503	HCT-116	colon:	n/a	chr4:48271163-48271172
16	MAFK	chr4:48272030-48273395	K562	blood:	n/a	chr4:48273198-48273213
17	BACH1	chr4:48272285-48272805	K562	blood:	n/a	n/a
18	EP300	chr4:48271984-48272537	K562	blood:	n/a	chr4:48272115-48272124
19	RELA	chr4:48271221-48273441	GM19193	blood:	n/a	n/a
20	POLR2A	chr4:48271148-48272531	GM15510	blood:	n/a	n/a
21	USF1	chr4:48272204-48272588	A549	lung:	n/a	chr4:48272386-48272407 chr4:48272391-48272400 chr4:48272390-48272401
22	UBTF	chr4:48271302-48272505	K562	blood:	n/a	n/a
23	FOXM1	chr4:48271892-48272612	GM12878	blood:	n/a	n/a
24	HDAC2	chr4:48271324-48272522	MCF-7	breast:	n/a	n/a
25	KAP1	chr4:48272095-48273922	HEK293	kidney:	n/a	n/a
26	POLR2A	chr4:48271343-48272565	K562	blood:	n/a	n/a
27	MAX	chr4:48270930-48272770	HCT-116	colon:	n/a	n/a
28	MTA3	chr4:48271915-48273593	GM12878	blood:	n/a	n/a
29	RUNX3	chr4:48270974-48272543	GM12878	blood:	n/a	n/a
30	ATF2	chr4:48272043-48272668	GM12878	blood:	n/a	n/a
31	NR2F2	chr4:48271156-48272984	K562	blood:	n/a	n/a
32	BHLHE40	chr4:48271106-48272528	HepG2	liver:	n/a	chr4:48272386-48272407 chr4:48272391-48272400 chr4:48271167-48271176 chr4:48271162-48271183
33	GABPA	chr4:48271666-48272527	MCF-7	breast:	n/a	n/a
34	MXI1	chr4:48272139-48272507	H1-hESC	embryonic stem cell:	n/a	n/a
35	MYC	chr4:48271194-48272553	NB4	blood:	n/a	n/a
36	USF1	chr4:48272153-48272518	SK-N-SH_RA	brain:	n/a	chr4:48272386-48272407 chr4:48272391-48272400 chr4:48272390-48272401
37	USF1	chr4:48272177-48272574	K562	blood:	n/a	chr4:48272386-48272407 chr4:48272391-48272400 chr4:48272390-48272401
38	MTA3	chr4:48272046-48272529	GM12878	blood:	n/a	n/a
39	NFIC	chr4:48271862-48272638	GM12878	blood:	n/a	n/a
40	POLR2A	chr4:48271568-48272504	MCF10A-Er-Src	breast:	n/a	n/a
41	EP300	chr4:48271968-48272535	GM12878	blood:	n/a	chr4:48272115-48272124
42	POLR2A	chr4:48271284-48272584	HL-60	blood:	n/a	n/a
43	POLR2A	chr4:48271584-48272607	GM12878	blood:	n/a	n/a
44	USF2	chr4:48272072-48272530	H1-hESC	embryonic stem cell:	n/a	chr4:48272390-48272401 chr4:48272386-48272407 chr4:48272391-48272400
45	ZNF143	chr4:48272029-48272622	K562	blood:	n/a	n/a
46	POU2F2	chr4:48272048-48272502	GM12891	blood:	n/a	n/a
47	POLR2A	chr4:48271307-48272510	HL-60	blood:	n/a	n/a
48	POLR2A	chr4:48271141-48272638	Raji	blood:	n/a	n/a
49	POLR2A	chr4:48271475-48272509	NB4	blood:	n/a	n/a
50	CEBPB	chr4:48271922-48272679	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:156392017..156392697-chr4:48272003..48272899,2	NB4	blood:
2	chr4:48270358..48273390-chr4:48340605..48344777,4	MCF-7	breast:
3	chr4:48270141..48273598-chr4:48341900..48344865,7	K562	blood:
4	chr4:48167349..48169980-chr4:48272046..48273556,2	K562	blood:
5	chr4:48272391..48273974-chr4:48279554..48281442,2	MCF-7	breast:
6	chr4:48269261..48273807-chr4:48342628..48344865,6	K562	blood:

Variant related genes	Relation type
TEC	TF binding region
ENSG00000163659	Chromatin interaction
ENSG00000109171	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10433686	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10433724	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11724334	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11732570	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11932069	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11934137	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12233640	0.80[AMR][1000 genomes]
rs12499189	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13143606	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1509655	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs170145	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1828297	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1848742	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1912162	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036766	0.81[ASN][1000 genomes]
rs2136503	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2353304	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2664024	0.84[EUR][1000 genomes]
rs2664027	0.84[EUR][1000 genomes]
rs2704409	0.84[EUR][1000 genomes]
rs309883	0.84[EUR][1000 genomes]
rs309891	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs309892	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs368292	0.84[EUR][1000 genomes]
rs373720	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs379323	0.84[EUR][1000 genomes]
rs430599	0.83[EUR][1000 genomes]
rs4529022	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4694892	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55656036	0.95[AMR][1000 genomes]
rs56041079	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56063319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58166553	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58372912	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59349478	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59741528	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59896383	0.89[AMR][1000 genomes]
rs62309361	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62309362	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62311498	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6447626	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6447627	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6836661	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6840958	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6852406	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6858850	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7657451	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7659044	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7665958	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7666809	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7688059	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7693991	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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:108 , 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	chr4:48270600-48272600	Active TSS	NHDF-Ad	bronchial
3	chr4:48270600-48272800	Active TSS	A549	lung
4	chr4:48270600-48272800	Active TSS	NHLF	lung
5	chr4:48270800-48272600	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr4:48270800-48272600	Active TSS	HSMMtube	muscle
7	chr4:48270800-48272800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr4:48270800-48272800	Active TSS	H9 Cell Line	embryonic stem cell
9	chr4:48270800-48272800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:48270800-48272800	Active TSS	Primary T cells from cord blood	blood
11	chr4:48270800-48272800	Active TSS	Rectal Smooth Muscle	rectum
12	chr4:48271000-48272600	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr4:48271000-48272600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:48271000-48272600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:48271000-48272600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:48271000-48272600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:48271000-48272600	Active TSS	Liver	Liver
18	chr4:48271000-48272600	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr4:48271000-48272600	Active TSS	Left Ventricle	heart
20	chr4:48271000-48272600	Active TSS	Psoas Muscle	Psoas
21	chr4:48271000-48272600	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr4:48271000-48272600	Bivalent/Poised TSS	HepG2	liver
23	chr4:48271000-48272600	Active TSS	HMEC	breast
24	chr4:48271000-48272800	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr4:48271000-48272800	Active TSS	Colon Smooth Muscle	Colon
26	chr4:48271200-48272600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:48271200-48272600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:48271200-48272600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:48271200-48272600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:48271200-48272600	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr4:48271200-48272600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:48271200-48272600	Active TSS	Muscle Satellite Cultured Cells	--
33	chr4:48271200-48272600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr4:48271200-48272600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:48271200-48272600	Active TSS	Aorta	Aorta
36	chr4:48271200-48272600	Active TSS	Brain Anterior Caudate	brain
37	chr4:48271200-48272600	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr4:48271200-48272600	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr4:48271200-48272600	Active TSS	Osteobl	bone
40	chr4:48271200-48272800	Active TSS	Brain Angular Gyrus	brain
41	chr4:48271200-48272800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:48271400-48272600	Active TSS	Brain Substantia Nigra	brain
43	chr4:48271600-48272600	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr4:48271600-48272600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr4:48271600-48273200	Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr4:48271800-48272600	Active TSS	HUVEC	blood vessel
47	chr4:48271800-48272800	Bivalent Enhancer	Dnd41	blood
48	chr4:48272000-48272600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr4:48272000-48272600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr4:48272000-48272600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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