Variant report

Variant	rs554012060
Chromosome Location	chr1:228674126-228674127
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	RFX5	chr1:228673704-228675743	IMR90	lung:	n/a	chr1:228674183-228674198
2	CREB1	chr1:228674063-228675219	GM12878	blood:	n/a	n/a
3	SIN3A	chr1:228674089-228675493	H1-hESC	embryonic stem cell:	n/a	chr1:228675461-228675472 chr1:228674871-228674882 chr1:228675386-228675399 chr1:228675388-228675399
4	MAX	chr1:228674036-228675210	ECC-1	luminal epithelium:	n/a	n/a
5	TAF1	chr1:228674046-228675272	H1-neurons	neurons:	n/a	n/a
6	SP1	chr1:228674046-228675375	HCT-116	colon:	n/a	chr1:228674571-228674585
7	POLR2A	chr1:228674081-228674853	U87	brain:	n/a	n/a
8	CREB1	chr1:228674085-228675272	K562	blood:	n/a	n/a
9	POLR2A	chr1:228674089-228676108	GM12892	blood:	n/a	n/a
10	TCF12	chr1:228674065-228675270	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr1:228674061-228674824	GM12892	blood:	n/a	n/a
12	POLR2A	chr1:228674014-228675771	H1-neurons	neurons:	n/a	n/a
13	ELF1	chr1:228674053-228675232	GM12878	blood:	n/a	chr1:228675200-228675212
14	RFX5	chr1:228673996-228675288	Hela-S3	cervix:	n/a	chr1:228674183-228674198
15	POU2F2	chr1:228674085-228675069	GM12878	blood:	n/a	chr1:228674572-228674584
16	CBX3	chr1:228674087-228675164	K562	blood:	n/a	n/a
17	POLR2A	chr1:228674112-228675348	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr1:228674056-228675431	GM12892	blood:	n/a	n/a
19	YY1	chr1:228674061-228675047	A549	lung:	n/a	n/a
20	CREB1	chr1:228674100-228675198	H1-hESC	embryonic stem cell:	n/a	n/a
21	RUNX3	chr1:228674081-228675156	GM12878	blood:	n/a	n/a
22	EP300	chr1:228674066-228674375	SK-N-SH_RA	brain:	n/a	n/a
23	REST	chr1:228673892-228675709	H1-neurons	neurons:	n/a	chr1:228675288-228675301 chr1:228675360-228675373
24	POLR2A	chr1:228673987-228675188	U87	brain:	n/a	n/a
25	MXI1	chr1:228673999-228676881	IMR90	lung:	n/a	n/a
26	POLR2A	chr1:228673803-228676876	HepG2	liver:	n/a	n/a
27	POLR2A	chr1:228673987-228675194	U87	brain:	n/a	n/a
28	GTF3C2	chr1:228673899-228675330	K562	blood:	n/a	n/a
29	POLR2A	chr1:228674113-228675018	HL-60	blood:	n/a	n/a
30	GTF3C2	chr1:228673808-228674638	Hela-S3	cervix:	n/a	n/a
31	TBP	chr1:228674120-228675038	GM12878	blood:	n/a	n/a
32	MYC	chr1:228674073-228675240	A549	lung:	n/a	n/a
33	CREB1	chr1:228674101-228675188	HepG2	liver:	n/a	n/a
34	CREB1	chr1:228674121-228675210	HepG2	liver:	n/a	n/a
35	POLR2A	chr1:228674108-228675375	PANC-1	pancreas:	n/a	n/a
36	EP300	chr1:228674107-228675268	ECC-1	luminal epithelium:	n/a	chr1:228675176-228675185 chr1:228675139-228675155 chr1:228675202-228675211
37	RFX5	chr1:228673914-228674967	H1-hESC	embryonic stem cell:	n/a	chr1:228674183-228674198
38	RFX5	chr1:228674018-228675023	GM12878	blood:	n/a	chr1:228674183-228674198
39	POLR2A	chr1:228674119-228674686	GM12891	blood:	n/a	n/a
40	SIN3AK20	chr1:228674065-228675333	MCF-7	breast:	n/a	n/a
41	PML	chr1:228674058-228675228	GM12878	blood:	n/a	n/a
42	NR2F2	chr1:228674057-228675186	K562	blood:	n/a	n/a
43	MYBL2	chr1:228674062-228675264	HepG2	liver:	n/a	n/a
44	RPC155	chr1:228673810-228674515	Hela-S3	cervix:	n/a	n/a
45	TAF1	chr1:228674126-228674459	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:228674071-228675407	GM12878	blood:	n/a	n/a
47	POLR2A	chr1:228674022-228675332	PFSK-1	brain:	n/a	n/a
48	MAX	chr1:228674106-228675241	A549	lung:	n/a	n/a
49	POLR2A	chr1:228674118-228674901	HepG2	liver:	n/a	n/a
50	MTA3	chr1:228674052-228675158	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:11967567..11969704-chr1:228673208..228675906,2	MCF-7	breast:
2	chr1:228642342..228647806-chr1:228672380..228678428,13	MCF-7	breast:
3	chr1:228671614..228676496-chr1:228676543..228681096,6	MCF-7	breast:
4	chr1:228672968..228678350-chr1:228679226..228685848,20	MCF-7	breast:
5	chr1:228643230..228649256-chr1:228671672..228678578,15	MCF-7	breast:
6	chr1:228673229..228674751-chr9:33024497..33026836,2	MCF-7	breast:
7	chr1:228645158..228646173-chr1:228673944..228674999,3	Hela-S3	cervix:
8	chr1:228321585..228323850-chr1:228673376..228675624,2	K562	blood:
9	chr1:228674038..228674538-chr12:77157330..77158605,3	HCT-116	colon:
10	chr1:228673889..228674721-chr17:79935373..79935994,2	HCT-116	colon:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP5-915N17.9.1-2	chr1:228673895-228674821	NONHSAT010027

Variant related genes	Relation type
RNF187	TF binding region
ENSG00000168159	Chromatin interaction
ENSG00000086061	Chromatin interaction
ENSG00000137074	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000227625	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000169696	Chromatin interaction
ENSG00000186908	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
9	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
11	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
12	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
13	esv3417507	chr1:228673529-228677127	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 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	chr1:228673600-228674200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:228673600-228674600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:228673600-228675800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:228673600-228675800	Active TSS	K562	blood
5	chr1:228673600-228676000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:228673600-228676000	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:228673600-228676000	Active TSS	A549	lung
8	chr1:228673600-228676000	Active TSS	Hela-S3	cervix
9	chr1:228673600-228676200	Active TSS	H9 Cell Line	embryonic stem cell
10	chr1:228673800-228674200	Flanking Active TSS	Primary B cells from peripheral blood	blood
11	chr1:228673800-228674200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:228673800-228674200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:228673800-228674200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:228673800-228674200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr1:228673800-228674200	Flanking Active TSS	Fetal Muscle Trunk	muscle
16	chr1:228673800-228674200	Flanking Active TSS	Fetal Stomach	stomach
17	chr1:228673800-228674200	Flanking Active TSS	Fetal Thymus	thymus
18	chr1:228673800-228674200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr1:228673800-228674200	Active TSS	HepG2	liver
20	chr1:228673800-228674400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr1:228673800-228674400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr1:228673800-228674400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:228673800-228674400	Active TSS	Brain Germinal Matrix	brain
24	chr1:228673800-228674400	Active TSS	Right Atrium	heart
25	chr1:228673800-228674400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr1:228673800-228674400	Active TSS	NH-A	brain
27	chr1:228673800-228674600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr1:228673800-228674800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr1:228673800-228675600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:228673800-228675800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:228673800-228675800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:228673800-228675800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:228673800-228675800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:228673800-228675800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:228673800-228675800	Active TSS	Brain Hippocampus Middle	brain
36	chr1:228673800-228675800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:228673800-228675800	Active TSS	Fetal Muscle Leg	muscle
38	chr1:228673800-228675800	Active TSS	GM12878-XiMat	blood
39	chr1:228673800-228676000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:228673800-228676000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:228673800-228676000	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr1:228673800-228676000	Active TSS	Primary T cells from cord blood	blood
43	chr1:228673800-228676000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:228673800-228676000	Active TSS	Muscle Satellite Cultured Cells	--
45	chr1:228673800-228676000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:228673800-228676000	Active TSS	Aorta	Aorta
47	chr1:228673800-228676000	Active TSS	Brain Cingulate Gyrus	brain
48	chr1:228673800-228676000	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr1:228673800-228676000	Active TSS	Colon Smooth Muscle	Colon
50	chr1:228673800-228676000	Active TSS	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links