Variant report

Variant	rs6559513
Chromosome Location	chr9:72004149-72004150
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71996842..72001188-chr9:72001690..72005051,4	MCF-7	breast:
2	chr9:71734709..71737586-chr9:72003144..72005018,2	MCF-7	breast:
3	chr9:71937269..71941011-chr9:72000572..72004392,4	MCF-7	breast:
4	chr9:71905657..71909249-chr9:72003453..72006230,4	MCF-7	breast:
5	chr9:71991902..71994131-chr9:72003113..72004905,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119139	Chromatin interaction
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10116389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746594	0.86[CEU][hapmap]
rs10746613	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10780334	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780344	0.93[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10780360	0.85[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs10780361	0.85[JPT][hapmap]
rs10867414	0.88[ASN][1000 genomes]
rs10867423	0.82[CEU][hapmap]
rs11138400	0.88[YRI][hapmap]
rs11138419	0.88[YRI][hapmap]
rs1331979	0.89[YRI][hapmap]
rs1334312	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1761290	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1812971	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1929896	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2244720	0.80[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2309431	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2777866	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2777878	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2781521	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2781522	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2781526	0.86[JPT][hapmap]
rs2781527	0.82[EUR][1000 genomes]
rs3858105	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3896424	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3934600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4237230	0.80[JPT][hapmap]
rs4237232	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4237233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4237234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4483220	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4484762	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4503164	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744886	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4744894	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744895	0.87[AFR][1000 genomes]
rs62570239	0.85[AFR][1000 genomes]
rs6559488	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6559489	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6559490	0.87[ASN][1000 genomes]
rs6559498	0.80[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6559512	0.92[CEU][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559516	0.86[JPT][hapmap]
rs6559525	0.83[ASN][1000 genomes]
rs6559527	0.93[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7019551	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7033674	0.86[JPT][hapmap]
rs7043451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7044071	0.82[JPT][hapmap]
rs7046199	0.82[CEU][hapmap]
rs7357615	0.90[YRI][hapmap]
rs7856778	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7866250	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9314682	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv893431	chr9:72003036-72048098	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71985400-72006600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr9:71991800-72012200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:71992000-72009800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr9:71992600-72006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:71992600-72006600	Weak transcription	Esophagus	oesophagus
6	chr9:71993000-72006600	Weak transcription	Brain Hippocampus Middle	brain
7	chr9:71994400-72006800	Weak transcription	Spleen	Spleen
8	chr9:71995000-72012600	Weak transcription	Aorta	Aorta
9	chr9:71996600-72004200	Weak transcription	Right Atrium	heart
10	chr9:71997200-72005000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:71997200-72006600	Weak transcription	HSMMtube	muscle
12	chr9:71997400-72007400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr9:71997400-72009800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:71997600-72006200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:71997600-72006600	Weak transcription	Fetal Lung	lung
16	chr9:71998200-72005400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
17	chr9:72000000-72005000	Strong transcription	Ovary	ovary
18	chr9:72000200-72004800	Enhancers	Pancreas	Pancrea
19	chr9:72000200-72005000	Strong transcription	Stomach Smooth Muscle	stomach
20	chr9:72000600-72006600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr9:72001000-72006600	Weak transcription	Lung	lung
22	chr9:72001600-72004400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
23	chr9:72001800-72006400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:72002200-72006400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:72002400-72005200	Genic enhancers	Fetal Heart	heart
26	chr9:72002400-72006000	Weak transcription	Colon Smooth Muscle	Colon
27	chr9:72002400-72006400	Weak transcription	Right Ventricle	heart
28	chr9:72002400-72006800	Weak transcription	Gastric	stomach
29	chr9:72002600-72006400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr9:72002800-72005000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr9:72002800-72012400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr9:72003200-72004400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr9:72003200-72005600	Weak transcription	Left Ventricle	heart
34	chr9:72003400-72004400	Weak transcription	Psoas Muscle	Psoas
35	chr9:72003400-72006000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:72003400-72006000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:72003400-72006400	Weak transcription	Adipose Nuclei	Adipose
38	chr9:72003400-72006400	Weak transcription	Brain Anterior Caudate	brain
39	chr9:72003400-72008400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr9:72003400-72010000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr9:72003400-72012400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr9:72003400-72012400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr9:72003600-72005400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:72003600-72006200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr9:72003600-72006400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr9:72003600-72006400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr9:72003600-72006400	Weak transcription	Fetal Stomach	stomach
48	chr9:72003600-72026200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr9:72003800-72006200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr9:72004000-72004200	ZNF genes & repeats	Brain Substantia Nigra	brain

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