Variant report

Variant	rs9942183
Chromosome Location	chr4:128553889-128553890
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	MXI1	chr4:128553384-128555334	SK-N-SH	brain:	n/a	chr4:128554034-128554049
2	STAT3	chr4:128553494-128554823	MCF10A-Er-Src	breast:	n/a	chr4:128554019-128554027 chr4:128554017-128554028
3	KAP1	chr4:128553718-128554346	U2OS	brain:	n/a	n/a
4	USF1	chr4:128553795-128554342	K562	blood:	n/a	chr4:128554082-128554093
5	USF1	chr4:128553817-128554329	A549	lung:	n/a	chr4:128554082-128554093
6	REST	chr4:128553369-128554705	H1-neurons	neurons:	n/a	n/a
7	CEBPB	chr4:128553465-128554576	A549	lung:	n/a	n/a
8	YY1	chr4:128553775-128554572	SK-N-SH_RA	brain:	n/a	chr4:128554111-128554130 chr4:128554118-128554128 chr4:128554106-128554128 chr4:128554117-128554125
9	MXI1	chr4:128553700-128554543	Hela-S3	cervix:	n/a	chr4:128554034-128554049
10	NFYA	chr4:128553819-128554247	Hela-S3	cervix:	n/a	chr4:128553985-128554000 chr4:128553986-128554000 chr4:128553985-128554000 chr4:128553988-128553998
11	YY1	chr4:128553841-128554531	A549	lung:	n/a	chr4:128554111-128554130 chr4:128554118-128554128 chr4:128554106-128554128 chr4:128554117-128554125
12	BHLHE40	chr4:128553763-128554278	K562	blood:	n/a	n/a
13	SIN3AK20	chr4:128553820-128554222	H1-hESC	embryonic stem cell:	n/a	n/a
14	USF1	chr4:128553815-128554457	SK-N-SH	brain:	n/a	chr4:128554082-128554093
15	SIN3AK20	chr4:128553569-128554538	MCF-7	breast:	n/a	n/a
16	MAX	chr4:128553550-128554596	ECC-1	luminal epithelium:	n/a	chr4:128554082-128554092
17	FOXP2	chr4:128553889-128554184	SK-N-MC	brain:	n/a	n/a
18	YY1	chr4:128553510-128554626	ECC-1	luminal epithelium:	n/a	chr4:128554111-128554130 chr4:128554118-128554128 chr4:128554106-128554128 chr4:128554117-128554125
19	MAX	chr4:128553528-128554659	ECC-1	luminal epithelium:	n/a	chr4:128554082-128554092
20	TAF1	chr4:128553755-128554304	SK-N-SH	brain:	n/a	n/a
21	USF1	chr4:128553800-128554310	H1-hESC	embryonic stem cell:	n/a	chr4:128554082-128554093
22	GTF2F1	chr4:128553598-128554780	Hela-S3	cervix:	n/a	n/a
23	USF1	chr4:128553686-128554600	HCT-116	colon:	n/a	chr4:128554082-128554093
24	MAX	chr4:128553866-128554545	H1-hESC	embryonic stem cell:	n/a	chr4:128554082-128554092
25	MAX	chr4:128553676-128554354	A549	lung:	n/a	chr4:128554082-128554092
26	SIN3AK20	chr4:128553730-128554358	K562	blood:	n/a	n/a
27	SIN3AK20	chr4:128553783-128554400	SK-N-SH	brain:	n/a	n/a
28	MAX	chr4:128553650-128554580	SK-N-SH	brain:	n/a	chr4:128554082-128554092
29	POLR2A	chr4:128553762-128554302	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr4:128553580-128554836	SK-N-MC	brain:	n/a	n/a
31	CEBPB	chr4:128553454-128554374	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr4:128553713-128554407	Hela-S3	cervix:	n/a	n/a
33	RCOR1	chr4:128553731-128554717	K562	blood:	n/a	n/a
34	TBP	chr4:128553749-128554376	Hela-S3	cervix:	n/a	n/a
35	YY1	chr4:128553856-128554375	HepG2	liver:	n/a	chr4:128554111-128554130 chr4:128554118-128554128 chr4:128554106-128554128 chr4:128554117-128554125
36	TBL1XR1	chr4:128553808-128554190	K562	blood:	n/a	n/a
37	RCOR1	chr4:128553750-128554287	HepG2	liver:	n/a	n/a
38	CEBPB	chr4:128553521-128554214	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr4:128553712-128554337	HCT-116	colon:	n/a	n/a
40	POLR2A	chr4:128553486-128555096	MCF10A-Er-Src	breast:	n/a	n/a
41	RCOR1	chr4:128553677-128554569	K562	blood:	n/a	n/a
42	MAX	chr4:128553607-128554598	H1-hESC	embryonic stem cell:	n/a	chr4:128554082-128554092
43	FOXA1	chr4:128553888-128554260	T-47D	breast:	n/a	n/a
44	CEBPB	chr4:128553380-128553963	A549	lung:	n/a	n/a
45	YY1	chr4:128553574-128554481	ECC-1	luminal epithelium:	n/a	chr4:128554111-128554130 chr4:128554118-128554128 chr4:128554106-128554128 chr4:128554117-128554125
46	MAFK	chr4:128553791-128554179	K562	blood:	n/a	n/a
47	POLR2A	chr4:128553786-128554594	Hela-S3	cervix:	n/a	n/a
48	USF1	chr4:128553869-128554276	SK-N-SH_RA	brain:	n/a	chr4:128554082-128554093
49	USF2	chr4:128553751-128554488	Hela-S3	cervix:	n/a	chr4:128554082-128554093
50	POLR2A	chr4:128553699-128554521	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:174967985..174968897-chr4:128553828..128554517,2	Hela-S3	cervix:
2	chr4:128553197..128555974-chr4:128981706..128984336,2	K562	blood:
3	chr4:128543078..128545882-chr4:128552977..128554729,2	MCF-7	breast:

Variant related genes	Relation type
INTU	TF binding region
ENSG00000116161	Chromatin interaction
ENSG00000164066	Chromatin interaction
ENSG00000138709	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs55856325	1.00[AMR][1000 genomes]
rs57569721	1.00[AMR][1000 genomes]
rs61002561	1.00[AMR][1000 genomes]
rs6827230	1.00[AMR][1000 genomes]
rs6836676	0.95[MKK][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847013	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847014	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847020	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73847024	1.00[AMR][1000 genomes]
rs73847026	1.00[AMR][1000 genomes]
rs7654838	1.00[AMR][1000 genomes]
rs7655450	1.00[ASW][hapmap];0.95[MKK][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs7689666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9942182	0.95[AFR][1000 genomes];1.00[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	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1029214	chr4:128292215-128683123	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537247	chr4:128292215-128683123	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv817326	chr4:128292216-128915201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv879916	chr4:128422400-128694288	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv879917	chr4:128478408-128841252	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv1800085	chr4:128502675-128557864	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv830056	chr4:128517139-128676557	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv879918	chr4:128543742-128694288	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv879919	chr4:128543742-128697519	Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128553000-128554800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr4:128553000-128555200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr4:128553200-128554000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:128553200-128554800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:128553200-128555400	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr4:128553200-128555800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr4:128553400-128554000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:128553400-128554000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr4:128553400-128554200	Active TSS	Brain Germinal Matrix	brain
10	chr4:128553400-128554400	ZNF genes & repeats	Fetal Brain Male	brain
11	chr4:128553400-128554600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr4:128553400-128554600	Bivalent/Poised TSS	Primary B cells from cord blood	blood
13	chr4:128553400-128554600	Active TSS	Fetal Heart	heart
14	chr4:128553400-128554600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr4:128553400-128554600	Bivalent/Poised TSS	HepG2	liver
16	chr4:128553400-128554800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr4:128553400-128554800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:128553400-128554800	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr4:128553400-128554800	Active TSS	Aorta	Aorta
20	chr4:128553400-128554800	Active TSS	Fetal Lung	lung
21	chr4:128553400-128554800	Active TSS	Fetal Muscle Leg	muscle
22	chr4:128553400-128554800	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr4:128553400-128554800	Active TSS	NH-A	brain
24	chr4:128553400-128555000	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr4:128553400-128555000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:128553400-128555000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr4:128553400-128555000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:128553400-128555000	Active TSS	Brain Anterior Caudate	brain
29	chr4:128553400-128555000	Active TSS	Brain Cingulate Gyrus	brain
30	chr4:128553400-128555000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:128553400-128555000	Active TSS	Brain Substantia Nigra	brain
32	chr4:128553400-128555000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr4:128553400-128555000	Active TSS	Fetal Kidney	kidney
34	chr4:128553400-128555000	Active TSS	Fetal Stomach	stomach
35	chr4:128553400-128555000	Active TSS	Psoas Muscle	Psoas
36	chr4:128553400-128555000	Active TSS	Stomach Smooth Muscle	stomach
37	chr4:128553400-128555000	Active TSS	A549	lung
38	chr4:128553400-128555000	Active TSS	Hela-S3	cervix
39	chr4:128553400-128555000	Active TSS	NHDF-Ad	bronchial
40	chr4:128553400-128555200	Active TSS	H1 Cell Line	embryonic stem cell
41	chr4:128553400-128555200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:128553400-128555200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:128553400-128555200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:128553400-128555200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:128553400-128555200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:128553400-128555200	Active TSS	Brain Hippocampus Middle	brain
47	chr4:128553400-128555200	Active TSS	Duodenum Mucosa	Duodenum
48	chr4:128553400-128555200	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr4:128553400-128555200	Active TSS	Fetal Intestine Large	intestine
50	chr4:128553400-128555200	Active TSS	Ovary	ovary

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