Variant report

Variant	rs538604
Chromosome Location	chr1:228605358-228605359
allele	A/T
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	STAT3	chr1:228605175-228605635	MCF10A-Er-Src	breast:	n/a	chr1:228605342-228605353
2	SRF	chr1:228605161-228605688	ECC-1	luminal epithelium:	n/a	n/a
3	STAT1	chr1:228605182-228605596	K562	blood:	n/a	chr1:228605342-228605353
4	STAT3	chr1:228605136-228605524	MCF10A-Er-Src	breast:	n/a	chr1:228605342-228605353
5	STAT5A	chr1:228605132-228605583	K562	blood:	n/a	n/a
6	STAT3	chr1:228605188-228605603	MCF10A-Er-Src	breast:	n/a	chr1:228605342-228605353
7	STAT3	chr1:228605204-228605626	MCF10A-Er-Src	breast:	n/a	chr1:228605342-228605353
8	SRF	chr1:228605225-228605561	K562	blood:	n/a	n/a
9	STAT5A	chr1:228605102-228605693	K562	blood:	n/a	n/a
10	STAT1	chr1:228604911-228605848	Hela-S3	cervix:	n/a	chr1:228605764-228605776 chr1:228605078-228605090 chr1:228605342-228605353

Variant related genes	Relation type
TRIM17	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10157289	0.80[EUR][1000 genomes]
rs10158354	0.80[EUR][1000 genomes]
rs10158680	0.80[EUR][1000 genomes]
rs10916314	0.91[CHB][hapmap]
rs11555960	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12031395	0.80[EUR][1000 genomes]
rs12061490	0.80[EUR][1000 genomes]
rs12061642	0.88[EUR][1000 genomes]
rs12065660	0.80[EUR][1000 genomes]
rs12065815	0.83[EUR][1000 genomes]
rs12082349	0.85[EUR][1000 genomes]
rs12085738	0.83[EUR][1000 genomes]
rs12089997	0.80[EUR][1000 genomes]
rs12093491	0.85[EUR][1000 genomes]
rs12094956	0.85[EUR][1000 genomes]
rs12131962	0.85[ASN][1000 genomes]
rs12691493	0.88[EUR][1000 genomes]
rs12735877	0.85[EUR][1000 genomes]
rs12760907	0.85[EUR][1000 genomes]
rs13373984	0.88[EUR][1000 genomes]
rs2230656	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3105114	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34090141	0.88[EUR][1000 genomes]
rs34673199	0.80[EUR][1000 genomes]
rs35155240	0.80[EUR][1000 genomes]
rs35711644	0.82[EUR][1000 genomes]
rs3738687	0.85[EUR][1000 genomes]
rs3795814	0.80[EUR][1000 genomes]
rs4065231	0.82[EUR][1000 genomes]
rs474600	0.88[EUR][1000 genomes]
rs491670	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs493950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs493954	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs494154	1.00[CEU][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs503203	0.89[EUR][1000 genomes]
rs503391	0.88[EUR][1000 genomes]
rs505129	0.83[EUR][1000 genomes]
rs513467	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs532465	0.88[EUR][1000 genomes]
rs541959	0.83[EUR][1000 genomes]
rs56174824	0.85[EUR][1000 genomes]
rs564309	0.88[EUR][1000 genomes]
rs572442	0.84[EUR][1000 genomes]
rs573128	0.84[EUR][1000 genomes]
rs58462432	0.81[EUR][1000 genomes]
rs61825312	0.80[EUR][1000 genomes]
rs61825336	0.88[EUR][1000 genomes]
rs61825338	0.87[EUR][1000 genomes]
rs6703500	0.83[ASN][1000 genomes]
rs7555298	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9787095	0.80[EUR][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:55 , 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	chr1:228603800-228605400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr1:228604200-228605400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
5	chr1:228604200-228605400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
6	chr1:228604200-228605600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:228604200-228605600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:228604200-228606000	Enhancers	Pancreas	Pancrea
9	chr1:228604400-228606200	Enhancers	Placenta Amnion	Placenta Amnion
10	chr1:228604400-228606200	Enhancers	HMEC	breast
11	chr1:228604600-228605400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr1:228604600-228605400	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr1:228604600-228605600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:228604600-228605600	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr1:228604600-228605600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:228604600-228605600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:228604600-228605600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:228604600-228605600	Bivalent Enhancer	Fetal Intestine Large	intestine
19	chr1:228604600-228605600	Bivalent Enhancer	Stomach Mucosa	stomach
20	chr1:228604600-228605800	Enhancers	Ovary	ovary
21	chr1:228604600-228606000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:228604600-228606400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:228604800-228605400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr1:228604800-228605400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr1:228604800-228605400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr1:228604800-228605400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:228604800-228605400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:228604800-228605400	Flanking Active TSS	NHEK	skin
29	chr1:228604800-228606000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:228604800-228606000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:228604800-228606200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:228604800-228606200	Enhancers	Fetal Heart	heart
33	chr1:228604800-228606600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:228605000-228605400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:228605000-228605400	Bivalent Enhancer	Brain Anterior Caudate	brain
36	chr1:228605000-228605600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
37	chr1:228605000-228605600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
38	chr1:228605000-228605600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
39	chr1:228605000-228605600	Bivalent Enhancer	Fetal Lung	lung
40	chr1:228605000-228606000	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr1:228605000-228606200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:228605000-228606200	Enhancers	Esophagus	oesophagus
43	chr1:228605000-228607200	Enhancers	K562	blood
44	chr1:228605200-228605400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
45	chr1:228605200-228605400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
46	chr1:228605200-228605400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
47	chr1:228605200-228605400	Bivalent Enhancer	Osteobl	bone
48	chr1:228605200-228605600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:228605200-228605600	Bivalent Enhancer	Primary T cells from cord blood	blood
50	chr1:228605200-228605600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links