Variant report

Variant	rs28632116
Chromosome Location	chr4:57253577-57253578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:499)
CpG islands
(count:61)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:499 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr4:57253248-57253866	GM12892	blood:	n/a	n/a
2	FOXA1	chr4:57253067-57253914	HepG2	liver:	n/a	chr4:57253342-57253357
3	TAF1	chr4:57253220-57253756	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:57253107-57253956	K562	blood:	n/a	n/a
5	POLR2A	chr4:57253034-57254017	K562	blood:	n/a	n/a
6	POLR2A	chr4:57253052-57253914	HCT-116	colon:	n/a	n/a
7	MAX	chr4:57253181-57253900	K562	blood:	n/a	n/a
8	CREB1	chr4:57253013-57254392	ECC-1	luminal epithelium:	n/a	n/a
9	REST	chr4:57253087-57254069	H1-neurons	neurons:	n/a	chr4:57253697-57253710 chr4:57253417-57253431 chr4:57253709-57253719
10	ELF1	chr4:57253382-57253821	A549	lung:	n/a	n/a
11	REST	chr4:57253323-57253737	SK-N-SH	brain:	n/a	chr4:57253697-57253710 chr4:57253417-57253431 chr4:57253709-57253719
12	MAX	chr4:57253275-57253903	HUVEC	blood vessel:	n/a	n/a
13	YY1	chr4:57253173-57253914	GM12892	blood:	n/a	chr4:57253713-57253727
14	TAF1	chr4:57253063-57253980	ECC-1	luminal epithelium:	n/a	n/a
15	MAZ	chr4:57253166-57254114	Hela-S3	cervix:	n/a	n/a
16	ATF3	chr4:57253444-57253884	A549	lung:	n/a	chr4:57253678-57253685 chr4:57253675-57253688 chr4:57253675-57253685 chr4:57253674-57253689 chr4:57253677-57253685 chr4:57253678-57253688 chr4:57253676-57253687 chr4:57253676-57253689 chr4:57253677-57253688 chr4:57253675-57253688
17	RFX5	chr4:57253156-57254223	Hela-S3	cervix:	n/a	n/a
18	MYC	chr4:57253134-57254193	K562	blood:	n/a	n/a
19	MAX	chr4:57253116-57254215	K562	blood:	n/a	n/a
20	ATF3	chr4:57253482-57253859	HepG2	liver:	n/a	chr4:57253678-57253685 chr4:57253675-57253688 chr4:57253675-57253685 chr4:57253674-57253689 chr4:57253677-57253685 chr4:57253678-57253688 chr4:57253676-57253687 chr4:57253676-57253689 chr4:57253677-57253688 chr4:57253675-57253688
21	TAF1	chr4:57252864-57254072	ECC-1	luminal epithelium:	n/a	n/a
22	SIX5	chr4:57253479-57253785	K562	blood:	n/a	n/a
23	RELA	chr4:57253161-57253967	GM18951	blood:	n/a	n/a
24	POU2F2	chr4:57253155-57253868	GM12891	blood:	n/a	n/a
25	TAF1	chr4:57253409-57253813	Hela-S3	cervix:	n/a	n/a
26	MAX	chr4:57253091-57254263	MCF-7	breast:	n/a	n/a
27	TAF1	chr4:57253212-57253877	PFSK-1	brain:	n/a	n/a
28	SP4	chr4:57253097-57253902	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAFK	chr4:57253121-57253799	HepG2	liver:	n/a	n/a
30	HCFC1	chr4:57253109-57254190	K562	blood:	n/a	n/a
31	JUND	chr4:57253240-57253869	A549	lung:	n/a	chr4:57253677-57253686
32	MBD4	chr4:57253070-57254000	HepG2	liver:	n/a	n/a
33	MAX	chr4:57253171-57254220	K562	blood:	n/a	n/a
34	POU2F2	chr4:57253157-57253900	GM12891	blood:	n/a	n/a
35	TBP	chr4:57252989-57254633	GM12878	blood:	n/a	n/a
36	SMC3	chr4:57253180-57253956	HepG2	liver:	n/a	n/a
37	POLR2A	chr4:57253130-57254255	Raji	blood:	n/a	n/a
38	MXI1	chr4:57253067-57254838	IMR90	lung:	n/a	n/a
39	CREB1	chr4:57253193-57253875	A549	lung:	n/a	n/a
40	REST	chr4:57253202-57253793	K562	blood:	n/a	chr4:57253697-57253710 chr4:57253417-57253431 chr4:57253709-57253719
41	ZNF263	chr4:57253271-57253858	HEK293-T-REx	kidney:	n/a	n/a
42	POLR2A	chr4:57253048-57254065	GM12892	blood:	n/a	n/a
43	PAX5	chr4:57253265-57253886	GM12878	blood:	n/a	chr4:57253775-57253784
44	MAX	chr4:57253165-57253934	H1-hESC	embryonic stem cell:	n/a	n/a
45	MXI1	chr4:57253290-57254771	K562	blood:	n/a	n/a
46	POLR2A	chr4:57253073-57254074	GM18505	blood:	n/a	n/a
47	POLR2A	chr4:57253128-57254003	PANC-1	pancreas:	n/a	n/a
48	SIN3AK20	chr4:57253454-57253916	PFSK-1	brain:	n/a	n/a
49	GATA2	chr4:57253226-57254306	SH-SY5Y	brain:	n/a	chr4:57253785-57253794
50	TAF1	chr4:57253134-57253854	GM12891	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:57253573-57253623	SKMC	muscle:	n/a
2	chr4:57253573-57253623	HEK293	kidney:	embryo
3	chr4:57253573-57253623	A549	lung:	n/a
4	chr4:57253573-57253623	HNPCEpiC	eye:	n/a
5	chr4:57253573-57253623	AG09319	gingival:	n/a
6	chr4:57253573-57253623	NHBE	bronchial:	n/a
7	chr4:57253573-57253623	PrEC	prostate:	n/a
8	chr4:57253573-57253623	K562	blood:	n/a
9	chr4:57253573-57253623	Caco-2	colon:	n/a
10	chr4:57253573-57253623	HPAEpiC	pulmonary alveolar:	n/a
11	chr4:57253573-57253623	MCF-7	breast:	n/a
12	chr4:57253573-57253623	NHDF-neo	bronchial:	n/a
13	chr4:57253573-57253623	HL-60	blood:	n/a
14	chr4:57253573-57253623	H1-hESC	embryonic stem cell:	embryo
15	chr4:57253573-57253623	AG09309	skin:	n/a
16	chr4:57253573-57253623	GM12878	blood:	n/a
17	chr4:57253573-57253623	HAEpiC	amniotic membrane:	n/a
18	chr4:57253573-57253623	T-47D	breast:	n/a
19	chr4:57253573-57253623	AG04449	skin:	fetal
20	chr4:57253573-57253623	GM19239	blood:	n/a
21	chr4:57253573-57253623	HMEC	breast:	n/a
22	chr4:57253573-57253623	HCF	heart:	n/a
23	chr4:57253573-57253623	MCF10A-Er-Src	breast:	n/a
24	chr4:57253573-57253623	GM12891	blood:	n/a
25	chr4:57253573-57253623	SAEC	small airway:	n/a
26	chr4:57253573-57253623	NT2-D1	testis:	n/a
27	chr4:57253573-57253623	CMK	blood:	n/a
28	chr4:57253573-57253623	ECC-1	luminal epithelium:	n/a
29	chr4:57253573-57253623	IMR90	lung:	fetal
30	chr4:57253573-57253623	PANC-1	pancreas:	n/a
31	chr4:57253573-57253623	AG10803	skin:	n/a
32	chr4:57253573-57253623	AoSMC	blood vessel:	n/a
33	chr4:57253573-57253623	HRPEpiC	eye:	n/a
34	chr4:57253573-57253623	HCPEpiC	choroid plexus:	n/a
35	chr4:57253573-57253623	Hela-S3	cervix:	n/a
36	chr4:57253573-57253623	ProgFib	skin:	n/a
37	chr4:57253573-57253623	HCM	heart:	n/a
38	chr4:57253573-57253623	HCT-116	colon:	n/a
39	chr4:57253573-57253623	ovcar-3	ovarian:	n/a
40	chr4:57253573-57253623	Jurkat	blood:	n/a
41	chr4:57253573-57253623	HepG2	liver:	n/a
42	chr4:57253573-57253623	GM12892	blood:	n/a
43	chr4:57253573-57253623	HUVEC	blood vessel:	n/a
44	chr4:57253573-57253623	SK-N-MC	brain:	n/a
45	chr4:57253573-57253623	Hepatocyte	liver:	n/a
46	chr4:57253573-57253623	BE2_C	brain:	n/a
47	chr4:57253573-57253623	AG04450	lung:	fetal
48	chr4:57253573-57253623	NH-A	brain:	n/a
49	chr4:57253573-57253623	HEEpiC	esophagus:	n/a
50	chr4:57253573-57253623	HRCEpiC	kidney:	n/a

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30987634..30988149-chr4:57253320..57254113,2	MCF-7	breast:
2	chr4:57252171..57255208-chr4:57332200..57335252,5	K562	blood:
3	chr4:57252130..57255932-chr4:57332416..57336369,6	K562	blood:
4	chr4:57251780..57255283-chr4:57300557..57304376,5	MCF-7	breast:
5	chr17:70588558..70589080-chr4:57253346..57253951,2	HCT-116	colon:
6	chr4:57250870..57256510-chr4:57298204..57303491,14	K562	blood:
7	chr4:57252113..57256281-chr4:57265528..57268374,5	MCF-7	breast:
8	chr3:49066605..49067149-chr4:57253167..57254108,2	Hela-S3	cervix:
9	chr4:57251940..57255035-chr4:57332077..57334754,4	MCF-7	breast:
10	chr4:57249593..57251737-chr4:57251842..57253742,2	K562	blood:
11	chr4:57252573..57255971-chr4:57298663..57303783,6	MCF-7	breast:
12	chr4:57251883..57253946-chr4:57396755..57399062,3	K562	blood:
13	chr4:56813904..56818311-chr4:57252529..57254894,5	K562	blood:
14	chr13:103498259..103499233-chr4:57253244..57254241,2	NB4	blood:
15	chr4:57251518..57253690-chr4:57313439..57315337,2	K562	blood:
16	chr17:36908664..36909384-chr4:57253348..57254053,2	Hela-S3	cervix:
17	chr4:57253370..57254122-chr4:171010791..171011707,2	HCT-116	colon:
18	chr4:57252051..57253870-chr9:33289300..33291783,2	K562	blood:
19	chr4:57253003..57253712-chr6:109415726..109416324,2	Hela-S3	cervix:
20	chr4:57252189..57254981-chr4:57775973..57777493,2	MCF-7	breast:
21	chr4:57250870..57256080-chr4:57298204..57304153,16	K562	blood:
22	chr2:26568529..26569521-chr4:57253361..57253888,2	MCF-7	breast:
23	chr4:57252303..57254207-chr4:57266105..57268233,2	MCF-7	breast:
24	chr4:57253354..57253885-chr7:25164472..25165128,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000269921	TF binding region
AASDH	TF binding region
ENSG00000269921	CpG island
AASDH	CpG island
ENSG00000100029	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000249693	Chromatin interaction
ENSG00000138018	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000134899	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000108294	Chromatin interaction
ENSG00000172115	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000174780	Chromatin interaction
ENSG00000174799	Chromatin interaction
ENSG00000086102	Chromatin interaction
ENSG00000183137	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000227036	Chromatin interaction
ENSG00000173567	Chromatin interaction
ENSG00000084093	Chromatin interaction
ENSG00000080546	Chromatin interaction
ENSG00000109576	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10007966	1.00[AMR][1000 genomes]
rs10018803	1.00[AFR][1000 genomes]
rs28501253	1.00[AMR][1000 genomes]
rs28558611	1.00[AMR][1000 genomes]
rs28623333	1.00[AMR][1000 genomes]
rs28651722	1.00[AMR][1000 genomes]
rs9994575	0.83[AFR][1000 genomes];1.00[AMR][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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 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	chr4:57251800-57254400	Active TSS	Hela-S3	cervix
2	chr4:57252200-57254400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr4:57252200-57254600	Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr4:57252200-57255000	Active TSS	NHLF	lung
5	chr4:57252200-57255200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr4:57252200-57255200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:57252200-57255200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr4:57252400-57254000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:57252400-57254200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:57252400-57254400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:57252400-57254400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:57252400-57254400	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr4:57252400-57254400	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr4:57252400-57254400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:57252400-57254400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:57252400-57254400	Active TSS	Fetal Intestine Small	intestine
17	chr4:57252400-57254400	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr4:57252400-57254400	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr4:57252400-57254400	Active TSS	Stomach Smooth Muscle	stomach
20	chr4:57252400-57254400	Active TSS	HSMM	muscle
21	chr4:57252400-57254400	Active TSS	NH-A	brain
22	chr4:57252400-57254600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:57252400-57255000	Active TSS	H1 Cell Line	embryonic stem cell
24	chr4:57252400-57255000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:57252400-57255000	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr4:57252400-57255000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:57252400-57255200	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr4:57252400-57255400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:57252400-57255600	Active TSS	K562	blood
30	chr4:57252600-57254000	Active TSS	Primary T cells from cord blood	blood
31	chr4:57252600-57254000	Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr4:57252600-57254000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr4:57252600-57254000	Active TSS	Adipose Nuclei	Adipose
34	chr4:57252600-57254000	Active TSS	Liver	Liver
35	chr4:57252600-57254200	Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr4:57252600-57254200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:57252600-57254200	Active TSS	Brain Germinal Matrix	brain
38	chr4:57252600-57254200	Active TSS	Duodenum Mucosa	Duodenum
39	chr4:57252600-57254200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr4:57252600-57254200	Active TSS	Placenta	Placenta
41	chr4:57252600-57254200	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr4:57252600-57254200	Active TSS	HUVEC	blood vessel
43	chr4:57252600-57254200	Active TSS	Monocytes-CD14+_RO01746	blood
44	chr4:57252600-57254400	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr4:57252600-57254400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:57252600-57254400	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr4:57252600-57254400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:57252600-57254400	Active TSS	Muscle Satellite Cultured Cells	--
49	chr4:57252600-57254400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:57252600-57254400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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