Variant report

Variant	rs60504719
Chromosome Location	chr4:2966987-2966988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr4:2966718-2967162	HEK293	kidney:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:2966982-2967032	AG10803	skin:	n/a
2	chr4:2966982-2967032	Hela-S3	cervix:	n/a
3	chr4:2966982-2967032	SK-N-SH	brain:	n/a
4	chr4:2966982-2967032	HUVEC	blood vessel:	n/a
5	chr4:2966982-2967032	CMK	blood:	n/a
6	chr4:2966982-2967032	GM06990	blood:	n/a
7	chr4:2966982-2967032	Caco-2	colon:	n/a
8	chr4:2966982-2967032	HRPEpiC	eye:	n/a
9	chr4:2966982-2967032	NHBE	bronchial:	n/a
10	chr4:2966982-2967032	HRE	kidney:	n/a
11	chr4:2966982-2967032	IMR90	lung:	fetal
12	chr4:2966982-2967032	HCT-116	colon:	n/a
13	chr4:2966982-2967032	AG09319	gingival:	n/a
14	chr4:2966982-2967032	GM12891	blood:	n/a
15	chr4:2966982-2967032	MCF-7	breast:	n/a
16	chr4:2966982-2967032	K562	blood:	n/a
17	chr4:2966982-2967032	SK-N-MC	brain:	n/a
18	chr4:2966982-2967032	AG04449	skin:	fetal
19	chr4:2966982-2967032	PANC-1	pancreas:	n/a
20	chr4:2966982-2967032	RPTEC	kidney:	n/a
21	chr4:2966982-2967032	MCF10A-Er-Src	breast:	n/a
22	chr4:2966982-2967032	HCPEpiC	choroid plexus:	n/a
23	chr4:2966982-2967032	T-47D	breast:	n/a
24	chr4:2966982-2967032	PrEC	prostate:	n/a
25	chr4:2966982-2967032	ECC-1	luminal epithelium:	n/a
26	chr4:2966982-2967032	NT2-D1	testis:	n/a
27	chr4:2966982-2967032	H1-hESC	embryonic stem cell:	embryo
28	chr4:2966982-2967032	HPAEpiC	pulmonary alveolar:	n/a
29	chr4:2966982-2967032	HEK293	kidney:	embryo
30	chr4:2966982-2967032	AoSMC	blood vessel:	n/a
31	chr4:2966982-2967032	GM12878	blood:	n/a
32	chr4:2966982-2967032	HCF	heart:	n/a
33	chr4:2966982-2967032	SKMC	muscle:	n/a
34	chr4:2966982-2967032	NH-A	brain:	n/a
35	chr4:2966982-2967032	HMEC	breast:	n/a
36	chr4:2966982-2967032	NB4	blood:	n/a
37	chr4:2966982-2967032	SK-N-SH_RA	brain:	n/a
38	chr4:2966982-2967032	Hepatocyte	liver:	n/a
39	chr4:2966982-2967032	HEEpiC	esophagus:	n/a
40	chr4:2966982-2967032	PFSK-1	brain:	n/a
41	chr4:2966982-2967032	HRCEpiC	kidney:	n/a
42	chr4:2966982-2967032	HAEpiC	amniotic membrane:	n/a
43	chr4:2966982-2967032	AG04450	lung:	fetal
44	chr4:2966982-2967032	HIPEpiC	eye:	n/a
45	chr4:2966982-2967032	HCM	heart:	n/a
46	chr4:2966982-2967032	GM19239	blood:	n/a
47	chr4:2966982-2967032	BE2_C	brain:	n/a
48	chr4:2966982-2967032	HL-60	blood:	n/a
49	chr4:2966982-2967032	Jurkat	blood:	n/a
50	chr4:2966982-2967032	HepG2	liver:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2962932..2965178-chr4:2965934..2967449,2	MCF-7	breast:
2	chr4:2963799..2967429-chr4:2967585..2973552,6	K562	blood:
3	chr4:2965936..2968451-chr4:2977512..2979704,2	K562	blood:
4	chr4:2965958..2968897-chr4:2971775..2974450,2	MCF-7	breast:

No data

Variant related genes	Relation type
NOP14	TF binding region
GRK4	TF binding region
NOP14	CpG island
GRK4	CpG island
ENSG00000087269	Chromatin interaction
ENSG00000125388	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12512648	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12696706	0.88[EUR][1000 genomes]
rs13103004	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13104559	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13104987	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13109886	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13111777	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13123779	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13132131	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1419043	0.83[ASN][1000 genomes]
rs1978031	0.82[ASN][1000 genomes]
rs1978032	0.82[ASN][1000 genomes]
rs34020100	0.88[EUR][1000 genomes]
rs34163500	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34540265	0.89[ASN][1000 genomes]
rs35163447	0.88[EUR][1000 genomes]
rs35781129	0.89[ASN][1000 genomes]
rs35909590	0.89[ASN][1000 genomes]
rs60635068	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6856669	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73189480	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv1008436	chr4:2947160-3031195	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv536998	chr4:2947160-3031195	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv593438	chr4:2948456-3030097	Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1008527	chr4:2957814-3019042	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1014013	chr4:2959876-3009507	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv536999	chr4:2959876-3009507	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv878453	chr4:2963222-3021383	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1008781	chr4:2964080-3019042	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv1003528	chr4:2964261-3011568	Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv537000	chr4:2964261-3011568	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2965800-2967200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr4:2966000-2967200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:2966000-2967200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:2966000-2967200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
5	chr4:2966200-2967000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:2966200-2967000	Weak transcription	Gastric	stomach
7	chr4:2966200-2967000	Enhancers	Small Intestine	intestine
8	chr4:2966200-2967400	Enhancers	Esophagus	oesophagus
9	chr4:2966200-2968200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:2966200-2970400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:2966200-2972200	Weak transcription	Aorta	Aorta
12	chr4:2966200-2977400	Weak transcription	Lung	lung
13	chr4:2966400-2967000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:2966400-2967000	Enhancers	Fetal Muscle Trunk	muscle
15	chr4:2966400-2967000	Enhancers	Fetal Muscle Leg	muscle
16	chr4:2966400-2967000	Enhancers	Fetal Stomach	stomach
17	chr4:2966400-2967000	Weak transcription	Pancreas	Pancrea
18	chr4:2966400-2967200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:2966400-2967200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr4:2966400-2967200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:2966400-2967200	Enhancers	Brain Cingulate Gyrus	brain
22	chr4:2966400-2967200	Active TSS	Brain Hippocampus Middle	brain
23	chr4:2966400-2968200	Weak transcription	Psoas Muscle	Psoas
24	chr4:2966400-2968800	Weak transcription	Fetal Intestine Small	intestine
25	chr4:2966400-2969400	Weak transcription	Placenta	Placenta
26	chr4:2966400-2970400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:2966400-2973200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:2966400-2974000	Weak transcription	Right Ventricle	heart
29	chr4:2966400-2974800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:2966400-2975600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:2966400-2978600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr4:2966400-2980200	Weak transcription	Left Ventricle	heart
33	chr4:2966400-2980200	Weak transcription	Ovary	ovary
34	chr4:2966400-2980400	Weak transcription	Spleen	Spleen
35	chr4:2966600-2967000	Enhancers	Brain Angular Gyrus	brain
36	chr4:2966600-2967000	Enhancers	Brain Anterior Caudate	brain
37	chr4:2966600-2967000	Enhancers	Fetal Heart	heart
38	chr4:2966600-2967200	Enhancers	Fetal Brain Male	brain
39	chr4:2966600-2967200	Enhancers	Dnd41	blood
40	chr4:2966600-2967200	Active TSS	HSMMtube	muscle
41	chr4:2966600-2967400	Enhancers	Primary hematopoietic stem cells	blood
42	chr4:2966600-2967600	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr4:2966600-2968400	Weak transcription	HMEC	breast
44	chr4:2966600-2969800	Weak transcription	HUVEC	blood vessel
45	chr4:2966600-2970400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:2966600-2970800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr4:2966600-2977600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr4:2966600-2978600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr4:2966600-2978800	Weak transcription	NH-A	brain
50	chr4:2966600-2979000	Weak transcription	HSMM	muscle

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