Variant report

Variant	rs60548274
Chromosome Location	chr1:190448006-190448007
allele	C/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	CTBP2	chr1:190447174-190448394	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF217	chr1:190447658-190448007	MCF-7	breast:	n/a	n/a
3	GATA3	chr1:190447596-190448108	MCF-7	breast:	n/a	n/a
4	TCF7L2	chr1:190447650-190448417	HEK293	kidney:	n/a	n/a
5	EBF1	chr1:190447422-190448028	GM12878	blood:	n/a	chr1:190447604-190447617 chr1:190447912-190447925 chr1:190447606-190447616 chr1:190447605-190447616 chr1:190447606-190447615 chr1:190447914-190447923 chr1:190447914-190447924 chr1:190447606-190447615 chr1:190447914-190447923
6	SIN3A	chr1:190447141-190448398	H1-hESC	embryonic stem cell:	n/a	n/a
7	GATA3	chr1:190447476-190448210	T-47D	breast:	n/a	n/a
8	KAP1	chr1:190447510-190448985	HEK293	kidney:	n/a	n/a
9	SP1	chr1:190447499-190448487	H1-hESC	embryonic stem cell:	n/a	chr1:190448028-190448040 chr1:190448029-190448039 chr1:190448028-190448039 chr1:190448030-190448039 chr1:190448029-190448038 chr1:190448029-190448043 chr1:190448028-190448040
10	HDAC2	chr1:190447629-190448105	MCF-7	breast:	n/a	n/a
11	POLR2A	chr1:190447267-190448073	H1-hESC	embryonic stem cell:	n/a	n/a
12	TBP	chr1:190447984-190448177	H1-hESC	embryonic stem cell:	n/a	n/a
13	REST	chr1:190446596-190448409	H1-neurons	neurons:	n/a	chr1:190447480-190447493 chr1:190448080-190448087 chr1:190447477-190447490 chr1:190447462-190447480 chr1:190447339-190447352 chr1:190447792-190447805 chr1:190447332-190447345
14	NANOG	chr1:190447870-190448202	H1-hESC	embryonic stem cell:	n/a	n/a
15	GATA2	chr1:190446768-190448262	SH-SY5Y	brain:	n/a	n/a
16	POLR2A	chr1:190447237-190448114	H1-neurons	neurons:	n/a	n/a
17	KAP1	chr1:190447723-190448915	U2OS	brain:	n/a	n/a
18	JUND	chr1:190447168-190448270	H1-hESC	embryonic stem cell:	n/a	chr1:190447519-190447527
19	EGR1	chr1:190447797-190448137	H1-hESC	embryonic stem cell:	n/a	chr1:190448032-190448042 chr1:190448030-190448045 chr1:190448031-190448044 chr1:190448031-190448044 chr1:190448029-190448039
20	TCF7L2	chr1:190446979-190448068	HCT-116	colon:	n/a	n/a
21	ZNF143	chr1:190447295-190448099	H1-hESC	embryonic stem cell:	n/a	chr1:190447438-190447456 chr1:190447337-190447355
22	POLR2A	chr1:190447639-190448270	SK-N-MC	brain:	n/a	n/a
23	GATA3	chr1:190447428-190448101	T-47D	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RGS18-5	chr1:190447888-190448066	NONHSAT008498

Variant related genes	Relation type
ENSG00000237457	TF binding region
BRINP3	TF binding region
ENSG00000241505	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs58160115	0.87[AFR][1000 genomes]
rs59070107	0.87[AFR][1000 genomes]
rs61426124	1.00[AFR][1000 genomes]
rs74130760	0.87[AFR][1000 genomes]
rs74130764	0.87[AFR][1000 genomes]
rs74130765	0.87[AFR][1000 genomes]
rs74130768	0.87[AFR][1000 genomes]
rs74130769	0.87[AFR][1000 genomes]
rs74130770	1.00[AFR][1000 genomes]
rs74130771	0.87[AFR][1000 genomes]
rs74130773	0.87[AFR][1000 genomes]
rs74130774	1.00[AFR][1000 genomes]
rs74130786	0.87[AFR][1000 genomes]
rs74130788	0.86[AFR][1000 genomes]
rs74130791	1.00[AFR][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	nsv932040	chr1:190005334-190914580	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv872758	chr1:190351677-190510003	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv872760	chr1:190377988-190577336	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872761	chr1:190389741-190485034	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv872762	chr1:190389741-190510003	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv872763	chr1:190389741-190531642	Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv872764	chr1:190399946-190531642	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv872765	chr1:190418653-190464647	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv466750	chr1:190433413-190496007	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv548551	chr1:190433413-190496007	Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv466761	chr1:190433413-190545283	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv548552	chr1:190433413-190545283	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv466772	chr1:190446253-190492280	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv548553	chr1:190446253-190492280	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:190440000-190448800	Active TSS	Duodenum Mucosa	Duodenum
2	chr1:190440200-190448800	Active TSS	Fetal Intestine Large	intestine
3	chr1:190440800-190448600	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr1:190440800-190448800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr1:190441200-190448600	Active TSS	Fetal Intestine Small	intestine
6	chr1:190441200-190448600	Active TSS	Right Atrium	heart
7	chr1:190443000-190449600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:190445200-190449000	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr1:190446200-190448800	Active TSS	Brain Germinal Matrix	brain
10	chr1:190446200-190449600	Active TSS	Brain Anterior Caudate	brain
11	chr1:190446200-190450000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:190446600-190448400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:190446800-190448400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:190446800-190448400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:190446800-190448400	Active TSS	Rectal Smooth Muscle	rectum
16	chr1:190447000-190448200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
17	chr1:190447000-190448200	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
18	chr1:190447000-190448400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr1:190447000-190448400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:190447000-190448400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:190447000-190448400	Bivalent/Poised TSS	Fetal Kidney	kidney
22	chr1:190447000-190448400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
23	chr1:190447000-190448400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
24	chr1:190447000-190448400	Bivalent/Poised TSS	A549	lung
25	chr1:190447000-190448600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:190447000-190448600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
27	chr1:190447000-190449400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:190447200-190448200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:190447200-190448200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:190447200-190448200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
31	chr1:190447200-190448200	Active TSS	Left Ventricle	heart
32	chr1:190447200-190448400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:190447200-190448400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:190447200-190448400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:190447200-190448400	Active TSS	Colon Smooth Muscle	Colon
36	chr1:190447200-190448400	Active TSS	Fetal Heart	heart
37	chr1:190447200-190448400	Active TSS	Right Ventricle	heart
38	chr1:190447200-190448400	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr1:190447200-190448400	Bivalent/Poised TSS	HSMM	muscle
40	chr1:190447200-190448400	Active TSS	NHDF-Ad	bronchial
41	chr1:190447200-190448400	Active TSS	NHLF	lung
42	chr1:190447200-190448600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr1:190447200-190448600	Active TSS	NH-A	brain
44	chr1:190447200-190449000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:190447200-190449000	Active TSS	Brain Cingulate Gyrus	brain
46	chr1:190447200-190449000	Active TSS	Fetal Brain Female	brain
47	chr1:190447200-190449200	Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr1:190447400-190448200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:190447400-190448200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:190447400-190448200	Bivalent Enhancer	Liver	Liver

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