Variant report

Variant	rs538851
Chromosome Location	chr1:228604248-228604249
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	TBP	chr1:228603924-228604262	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:228604065-228604324	HUVEC	blood vessel:	n/a	n/a
3	CTCF	chr1:228604140-228604290	NHDF-neo	bronchial:	n/a	chr1:228604197-228604218
4	CTCF	chr1:228604240-228604390	GM12870	blood:	n/a	n/a
5	MAX	chr1:228603787-228604364	H1-hESC	embryonic stem cell:	n/a	n/a
6	JUND	chr1:228604178-228604314	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr1:228603912-228604271	H1-hESC	embryonic stem cell:	n/a	chr1:228604197-228604218
8	CCNT2	chr1:228604229-228604266	K562	blood:	n/a	n/a
9	POLR2A	chr1:228603329-228604380	PANC-1	pancreas:	n/a	n/a
10	RAD21	chr1:228603927-228604254	H1-hESC	embryonic stem cell:	n/a	chr1:228604122-228604136 chr1:228604196-228604215
11	CTCF	chr1:228603848-228604264	H1-hESC	embryonic stem cell:	n/a	chr1:228604197-228604218
12	E2F6	chr1:228603846-228604421	H1-hESC	embryonic stem cell:	n/a	chr1:228604216-228604225 chr1:228603924-228603934 chr1:228604131-228604143 chr1:228604395-228604405 chr1:228604408-228604417
13	ZNF143	chr1:228603882-228604249	H1-hESC	embryonic stem cell:	n/a	chr1:228604139-228604157 chr1:228604125-228604135
14	GABPA	chr1:228603803-228604355	H1-hESC	embryonic stem cell:	n/a	n/a
15	E2F6	chr1:228603804-228604456	H1-hESC	embryonic stem cell:	n/a	chr1:228604216-228604225 chr1:228603924-228603934 chr1:228604131-228604143 chr1:228604395-228604405 chr1:228604408-228604417
16	RAD21	chr1:228603856-228604266	H1-hESC	embryonic stem cell:	n/a	chr1:228604122-228604136 chr1:228604196-228604215
17	MXI1	chr1:228603223-228605202	SK-N-SH	brain:	n/a	chr1:228603755-228603770
18	JUND	chr1:228603962-228604308	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr1:228603340-228604315	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:228603827-228604271	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr1:228604243-228604269	H1-hESC	embryonic stem cell:	n/a	n/a
22	ZBTB7A	chr1:228604141-228604437	K562	blood:	n/a	n/a
23	POLR2A	chr1:228603788-228604386	HUVEC	blood vessel:	n/a	n/a
24	CTCF	chr1:228603460-228604521	SK-N-SH	brain:	n/a	chr1:228604197-228604218
25	SIN3A	chr1:228603730-228604261	H1-hESC	embryonic stem cell:	n/a	chr1:228603994-228604007
26	BACH1	chr1:228603651-228604322	H1-hESC	embryonic stem cell:	n/a	n/a
27	RAD21	chr1:228603881-228604285	H1-hESC	embryonic stem cell:	n/a	chr1:228604122-228604136 chr1:228604196-228604215

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:228604240-228604290	BJ	skin:	n/a
2	chr1:228604240-228604290	MCF10A-Er-Src	breast:	n/a
3	chr1:228604240-228604290	HRPEpiC	eye:	n/a
4	chr1:228604240-228604290	HPAEpiC	pulmonary alveolar:	n/a
5	chr1:228604240-228604290	AG09309	skin:	n/a
6	chr1:228604240-228604290	AG04450	lung:	fetal
7	chr1:228604240-228604290	BE2_C	brain:	n/a
8	chr1:228604240-228604290	Hepatocyte	liver:	n/a
9	chr1:228604240-228604290	SKMC	muscle:	n/a
10	chr1:228604240-228604290	AG10803	skin:	n/a
11	chr1:228604240-228604290	A549	lung:	n/a
12	chr1:228604240-228604290	HNPCEpiC	eye:	n/a
13	chr1:228604240-228604290	SK-N-MC	brain:	n/a
14	chr1:228604240-228604290	NHDF-neo	bronchial:	n/a
15	chr1:228604240-228604290	K562	blood:	n/a
16	chr1:228604240-228604290	HL-60	blood:	n/a
17	chr1:228604240-228604290	HAEpiC	amniotic membrane:	n/a
18	chr1:228604240-228604290	T-47D	breast:	n/a
19	chr1:228604240-228604290	H1-hESC	embryonic stem cell:	embryo
20	chr1:228604240-228604290	PFSK-1	brain:	n/a
21	chr1:228604240-228604290	AG09319	gingival:	n/a
22	chr1:228604240-228604290	HUVEC	blood vessel:	n/a
23	chr1:228604240-228604290	SK-N-SH_RA	brain:	n/a
24	chr1:228604240-228604290	HMEC	breast:	n/a
25	chr1:228604240-228604290	Caco-2	colon:	n/a
26	chr1:228604240-228604290	HCF	heart:	n/a
27	chr1:228604240-228604290	HCM	heart:	n/a
28	chr1:228604240-228604290	NT2-D1	testis:	n/a
29	chr1:228604240-228604290	AoSMC	blood vessel:	n/a
30	chr1:228604240-228604290	U87	brain:	n/a
31	chr1:228604240-228604290	SAEC	small airway:	n/a
32	chr1:228604240-228604290	PrEC	prostate:	n/a
33	chr1:228604240-228604290	GM12878	blood:	n/a
34	chr1:228604240-228604290	GM06990	blood:	n/a
35	chr1:228604240-228604290	HIPEpiC	eye:	n/a
36	chr1:228604240-228604290	GM12891	blood:	n/a
37	chr1:228604240-228604290	RPTEC	kidney:	n/a
38	chr1:228604240-228604290	IMR90	lung:	fetal
39	chr1:228604240-228604290	HRCEpiC	kidney:	n/a
40	chr1:228604240-228604290	HCT-116	colon:	n/a
41	chr1:228604240-228604290	ECC-1	luminal epithelium:	n/a
42	chr1:228604240-228604290	Hela-S3	cervix:	n/a
43	chr1:228604240-228604290	NB4	blood:	n/a
44	chr1:228604240-228604290	Jurkat	blood:	n/a
45	chr1:228604240-228604290	HCPEpiC	choroid plexus:	n/a
46	chr1:228604240-228604290	NH-A	brain:	n/a
47	chr1:228604240-228604290	ovcar-3	ovarian:	n/a
48	chr1:228604240-228604290	HEEpiC	esophagus:	n/a
49	chr1:228604240-228604290	AG04449	skin:	fetal
50	chr1:228604240-228604290	PANC-1	pancreas:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228585219..228604537-chr1:228641966..228650471,45	MCF-7	breast:

Variant related genes	Relation type
TRIM17	TF binding region
TRIM17	CpG island
ENSG00000266174	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000196890	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1150917	0.85[ASN][1000 genomes]
rs1150918	0.88[ASN][1000 genomes]
rs1188473	0.86[ASN][1000 genomes]
rs1188474	0.84[ASN][1000 genomes]
rs12061642	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12065815	0.81[EUR][1000 genomes]
rs12082349	0.83[EUR][1000 genomes]
rs12085738	0.81[EUR][1000 genomes]
rs12093491	0.83[EUR][1000 genomes]
rs12094956	0.83[EUR][1000 genomes]
rs12691493	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12735877	0.83[EUR][1000 genomes]
rs12760907	0.83[EUR][1000 genomes]
rs13373984	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2230656	0.85[ASN][1000 genomes]
rs34090141	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3738687	0.83[EUR][1000 genomes]
rs474600	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs503203	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs503391	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs505129	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs532465	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs541959	0.81[EUR][1000 genomes]
rs56174824	0.83[EUR][1000 genomes]
rs564309	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs572442	0.82[EUR][1000 genomes]
rs573128	0.82[EUR][1000 genomes]
rs58462432	0.84[ASN][1000 genomes]
rs61825336	0.86[EUR][1000 genomes]
rs61825338	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	nsv470780	chr1:228464248-228606965	Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	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
12	nsv873281	chr1:228505739-228656780	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
13	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
14	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
15	nsv508697	chr1:228540037-228622614	Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
16	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
17	esv3325014	chr1:228603354-228605902	Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	esv3430608	chr1:228603354-228605902	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228596400-228615400	Weak transcription	A549	lung
2	chr1:228603000-228605400	Enhancers	Lung	lung
3	chr1:228603400-228604400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:228603400-228604400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
5	chr1:228603400-228604400	Bivalent Enhancer	Fetal Thymus	thymus
6	chr1:228603400-228605000	Enhancers	Gastric	stomach
7	chr1:228603600-228604400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr1:228603600-228604400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
9	chr1:228603600-228604400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
10	chr1:228603600-228604400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:228603600-228604400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:228603600-228604400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
13	chr1:228603600-228604400	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
14	chr1:228603600-228604400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
15	chr1:228603600-228604400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
16	chr1:228603600-228604400	Bivalent Enhancer	Stomach Mucosa	stomach
17	chr1:228603600-228604400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
18	chr1:228603600-228604400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
19	chr1:228603600-228604600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
20	chr1:228603600-228604600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr1:228603600-228604600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:228603600-228604600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:228603600-228604600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
24	chr1:228603600-228604800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
25	chr1:228603600-228605000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
26	chr1:228603600-228605000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
27	chr1:228603600-228605200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
28	chr1:228603800-228604400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:228603800-228604400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:228603800-228604400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:228603800-228604400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
32	chr1:228603800-228604400	Flanking Active TSS	HMEC	breast
33	chr1:228603800-228604400	Bivalent/Poised TSS	HSMM	muscle
34	chr1:228603800-228604600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:228603800-228604600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:228603800-228604600	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:228603800-228604600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:228603800-228604600	Flanking Active TSS	Right Ventricle	heart
39	chr1:228603800-228604600	Bivalent/Poised TSS	Thymus	Thymus
40	chr1:228603800-228604800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
41	chr1:228603800-228604800	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr1:228603800-228604800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
43	chr1:228603800-228605000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr1:228603800-228605000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
45	chr1:228603800-228605000	Weak transcription	K562	blood
46	chr1:228603800-228605200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
47	chr1:228603800-228605200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
48	chr1:228603800-228605400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
49	chr1:228604000-228604400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:228604000-228604400	Bivalent Enhancer	Adipose Nuclei	Adipose

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