Variant report

Variant	rs28656215
Chromosome Location	chr4:3077985-3077986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:3076758-3078137	GM12891	blood:	n/a	n/a
2	POLR2A	chr4:3075066-3078105	GM15510	blood:	n/a	n/a
3	POLR2A	chr4:3076094-3078808	GM12878	blood:	n/a	n/a
4	PML	chr4:3076003-3078213	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:3075327-3080089	GM18505	blood:	n/a	n/a
6	POLR2A	chr4:3077982-3078035	MCF10A-Er-Src	breast:	n/a	n/a
7	RUNX3	chr4:3076776-3078119	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:3076054-3080438	GM12891	blood:	n/a	n/a
9	WRNIP1	chr4:3077447-3078108	GM12878	blood:	n/a	n/a
10	RELA	chr4:3077008-3078516	GM18505	blood:	n/a	n/a
11	FOXM1	chr4:3076919-3078036	GM12878	blood:	n/a	n/a
12	STAT5A	chr4:3076785-3078582	GM12878	blood:	n/a	chr4:3077371-3077383 chr4:3077377-3077389 chr4:3077370-3077382 chr4:3077381-3077393
13	BCLAF1	chr4:3077412-3078618	GM12878	blood:	n/a	chr4:3077949-3077958
14	POLR2A	chr4:3077382-3078844	GM12891	blood:	n/a	n/a
15	RELA	chr4:3076849-3078101	GM12891	blood:	n/a	n/a
16	POLR2A	chr4:3075462-3078579	GM19099	blood:	n/a	n/a
17	POLR2A	chr4:3076082-3078168	GM12878	blood:	n/a	n/a
18	POLR2A	chr4:3076761-3078663	GM12892	blood:	n/a	n/a
19	POLR2A	chr4:3076751-3078175	GM12891	blood:	n/a	n/a
20	POLR2A	chr4:3076807-3078064	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:3076709-3078252	GM12892	blood:	n/a	n/a
22	NFATC1	chr4:3077331-3078201	GM12878	blood:	n/a	n/a
23	TBP	chr4:3077005-3078144	GM12878	blood:	n/a	n/a
24	POLR2A	chr4:3077379-3078136	GM12891	blood:	n/a	n/a
25	TBL1XR1	chr4:3077150-3078013	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:3076692-3078231	GM12878	blood:	n/a	n/a
27	BCLAF1	chr4:3077356-3078153	GM12878	blood:	n/a	chr4:3077368-3077381 chr4:3077949-3077958 chr4:3077376-3077389
28	RELA	chr4:3076956-3078022	GM19099	blood:	n/a	n/a
29	MAFK	chr4:3077929-3078113	H1-hESC	embryonic stem cell:	n/a	n/a
30	CHD1	chr4:3076963-3078549	GM12878	blood:	n/a	chr4:3077381-3077391 chr4:3076978-3076988 chr4:3077035-3077044
31	TAF1	chr4:3076758-3078044	GM12878	blood:	n/a	n/a
32	NFATC1	chr4:3077402-3078763	GM12878	blood:	n/a	n/a
33	POLR2A	chr4:3075485-3078087	GM18526	blood:	n/a	n/a
34	POLR2A	chr4:3076003-3078229	GM12892	blood:	n/a	n/a
35	POLR2A	chr4:3076749-3078162	GM12892	blood:	n/a	n/a
36	MXI1	chr4:3076958-3078211	GM12878	blood:	n/a	n/a
37	JUN	chr4:3076806-3078073	K562	blood:	n/a	chr4:3077379-3077388 chr4:3077378-3077387 chr4:3077376-3077385
38	POLR2A	chr4:3075409-3078093	GM18951	blood:	n/a	n/a
39	POLR2A	chr4:3075136-3078100	GM12892	blood:	n/a	n/a
40	MTA3	chr4:3076693-3080356	GM12878	blood:	n/a	n/a
41	ATF2	chr4:3076902-3078066	GM12878	blood:	n/a	n/a
42	POLR2A	chr4:3076052-3080484	GM12878	blood:	n/a	n/a
43	POLR2A	chr4:3076744-3078895	GM12878	blood:	n/a	n/a
44	POLR2A	chr4:3077651-3078050	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:3077939-3077989	GM19239	blood:	n/a
2	chr4:3077939-3077989	SK-N-SH	brain:	n/a
3	chr4:3077939-3077989	SK-N-SH_RA	brain:	n/a
4	chr4:3077939-3077989	A549	lung:	n/a
5	chr4:3077939-3077989	Hela-S3	cervix:	n/a
6	chr4:3077939-3077989	SAEC	small airway:	n/a
7	chr4:3077939-3077989	HUVEC	blood vessel:	n/a
8	chr4:3077939-3077989	PrEC	prostate:	n/a
9	chr4:3077939-3077989	PANC-1	pancreas:	n/a
10	chr4:3077939-3077989	HAEpiC	amniotic membrane:	n/a
11	chr4:3077939-3077989	AG10803	skin:	n/a
12	chr4:3077939-3077989	RPTEC	kidney:	n/a
13	chr4:3077939-3077989	HL-60	blood:	n/a
14	chr4:3077939-3077989	Jurkat	blood:	n/a
15	chr4:3077939-3077989	HEK293	kidney:	embryo
16	chr4:3077939-3077989	Caco-2	colon:	n/a
17	chr4:3077939-3077989	AoSMC	blood vessel:	n/a
18	chr4:3077939-3077989	LNCaP	prostate:	n/a
19	chr4:3077939-3077989	H1-hESC	embryonic stem cell:	embryo
20	chr4:3077939-3077989	SK-N-MC	brain:	n/a
21	chr4:3077939-3077989	PFSK-1	brain:	n/a
22	chr4:3077939-3077989	HCT-116	colon:	n/a
23	chr4:3077939-3077989	Hepatocyte	liver:	n/a
24	chr4:3077939-3077989	MCF-7	breast:	n/a
25	chr4:3077939-3077989	MCF10A-Er-Src	breast:	n/a
26	chr4:3077939-3077989	ProgFib	skin:	n/a
27	chr4:3077939-3077989	AG04449	skin:	fetal
28	chr4:3077939-3077989	T-47D	breast:	n/a
29	chr4:3077939-3077989	HEEpiC	esophagus:	n/a
30	chr4:3077939-3077989	NHBE	bronchial:	n/a
31	chr4:3077939-3077989	HMEC	breast:	n/a
32	chr4:3077939-3077989	CMK	blood:	n/a
33	chr4:3077939-3077989	NHDF-neo	bronchial:	n/a
34	chr4:3077939-3077989	GM06990	blood:	n/a
35	chr4:3077939-3077989	IMR90	lung:	fetal
36	chr4:3077939-3077989	BE2_C	brain:	n/a
37	chr4:3077939-3077989	GM12891	blood:	n/a
38	chr4:3077939-3077989	HIPEpiC	eye:	n/a
39	chr4:3077939-3077989	HCM	heart:	n/a
40	chr4:3077939-3077989	HNPCEpiC	eye:	n/a
41	chr4:3077939-3077989	AG09319	gingival:	n/a
42	chr4:3077939-3077989	NT2-D1	testis:	n/a
43	chr4:3077939-3077989	HCF	heart:	n/a
44	chr4:3077939-3077989	SKMC	muscle:	n/a
45	chr4:3077939-3077989	ECC-1	luminal epithelium:	n/a
46	chr4:3077939-3077989	NH-A	brain:	n/a
47	chr4:3077939-3077989	HCPEpiC	choroid plexus:	n/a
48	chr4:3077939-3077989	U87	brain:	n/a
49	chr4:3077939-3077989	GM12892	blood:	n/a
50	chr4:3077939-3077989	GM12878	blood:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr4:3074016..3078502-chr4:3111809..3117809,7	MCF-7	breast:
2	chr4:3076425..3077993-chr4:3087345..3089440,2	MCF-7	breast:
3	chr4:3076858..3078560-chr4:3090552..3093969,4	MCF-7	breast:
4	chr4:3076735..3079040-chr4:3100560..3102807,2	K562	blood:
5	chr4:3076522..3079094-chr4:3136211..3138250,2	MCF-7	breast:
6	chr4:2935808..2938115-chr4:3076304..3078834,3	K562	blood:
7	chr4:3076560..3079556-chr4:3107118..3109310,3	MCF-7	breast:
8	chr4:2935808..2937729-chr4:3076912..3078834,2	K562	blood:

No data

Variant related genes	Relation type
HTT-AS	TF binding region
HTT-AS	CpG island
ENSG00000109736	Chromatin interaction
ENSG00000249673	Chromatin interaction
ENSG00000197386	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12506200	0.81[ASN][1000 genomes]
rs13102260	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13122415	0.98[ASN][1000 genomes]
rs13141939	0.90[EUR][1000 genomes]
rs35631490	0.96[ASN][1000 genomes]
rs9996199	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	esv3406168	chr4:3075379-3078127	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr4:3074800-3078600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr4:3075000-3078400	Active TSS	A549	lung
3	chr4:3075200-3078000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:3075200-3078600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:3075400-3079800	Active TSS	GM12878-XiMat	blood
6	chr4:3075600-3078000	Active TSS	HepG2	liver
7	chr4:3075800-3078200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:3075800-3078200	Active TSS	HMEC	breast
9	chr4:3076800-3078000	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr4:3076800-3078000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:3076800-3078000	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr4:3076800-3078600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr4:3077000-3078000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr4:3077000-3078000	Flanking Active TSS	Fetal Muscle Trunk	muscle
15	chr4:3077200-3078200	Enhancers	Stomach Mucosa	stomach
16	chr4:3077200-3078400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:3077200-3078400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr4:3077200-3081000	Weak transcription	Spleen	Spleen
19	chr4:3077400-3078000	Enhancers	Primary T cells fromperipheralblood	blood
20	chr4:3077400-3078000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr4:3077400-3078000	Flanking Active TSS	Liver	Liver
22	chr4:3077400-3078000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
23	chr4:3077400-3078000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:3077400-3078000	Flanking Active TSS	Colonic Mucosa	Colon
25	chr4:3077400-3078000	Flanking Active TSS	Fetal Heart	heart
26	chr4:3077400-3078000	Flanking Active TSS	Fetal Thymus	thymus
27	chr4:3077400-3078000	Enhancers	Pancreas	Pancrea
28	chr4:3077400-3078000	Flanking Active TSS	Rectal Smooth Muscle	rectum
29	chr4:3077400-3078000	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr4:3077400-3078000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr4:3077400-3078000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr4:3077400-3078000	Flanking Active TSS	K562	blood
33	chr4:3077400-3078200	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr4:3077400-3078200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr4:3077400-3078200	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr4:3077400-3078200	Enhancers	Brain Substantia Nigra	brain
37	chr4:3077400-3078200	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr4:3077400-3078200	Flanking Active TSS	Fetal Lung	lung
39	chr4:3077400-3078200	Flanking Active TSS	Fetal Stomach	stomach
40	chr4:3077400-3078200	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr4:3077400-3078200	Flanking Active TSS	HSMM	muscle
42	chr4:3077400-3078200	Flanking Active TSS	Osteobl	bone
43	chr4:3077400-3078400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:3077400-3078400	Flanking Active TSS	Dnd41	blood
45	chr4:3077400-3078600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:3077400-3078600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:3077400-3078600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:3077400-3078600	Enhancers	Small Intestine	intestine
49	chr4:3077400-3079600	Weak transcription	Gastric	stomach
50	chr4:3077400-3093800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links