Variant report

Variant	rs2781521
Chromosome Location	chr9:72012341-72012342
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:72009613..72012397-chr9:72013386..72015808,3	MCF-7	breast:
2	chr9:72000714..72007830-chr9:72009954..72019278,14	MCF-7	breast:
3	chr9:72008297..72012521-chr9:72012809..72015808,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10116389	0.80[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10746594	0.87[CEU][hapmap];0.84[YRI][hapmap]
rs10746613	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780334	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10780344	0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10780360	0.86[JPT][hapmap]
rs10780361	0.86[JPT][hapmap]
rs10867423	0.82[CEU][hapmap]
rs11138491	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1334312	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1761290	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1812971	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1929896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244720	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2309431	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2777866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2781522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2781526	0.87[JPT][hapmap]
rs2781527	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2781529	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35625426	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3858105	0.82[CEU][hapmap];0.93[JPT][hapmap]
rs3896424	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934600	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4237232	0.87[ASN][1000 genomes]
rs4237233	0.81[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4237234	0.81[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4483220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4503164	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4744886	0.87[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap]
rs4744894	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62570234	0.82[ASN][1000 genomes]
rs62570235	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs62570236	0.82[ASN][1000 genomes]
rs62570237	0.82[ASN][1000 genomes]
rs6559488	0.87[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap]
rs6559489	0.82[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap]
rs6559498	0.82[CEU][hapmap];0.92[GIH][hapmap];0.84[LWK][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs6559512	0.92[CEU][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6559513	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6559516	0.87[JPT][hapmap]
rs6559525	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6559527	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7019551	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs7033674	0.87[JPT][hapmap]
rs7043451	0.84[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap]
rs7046199	0.82[CEU][hapmap];0.84[YRI][hapmap]
rs7856778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866250	0.87[CEU][hapmap];0.92[GIH][hapmap];0.84[LWK][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs9314682	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv8522	chr9:72009272-72034735	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2781521	TJP2	cis	parietal	SCAN
rs2781521	KLF9	cis	cerebellum	SCAN
rs2781521	TJP2	cis	cerebellum	SCAN
rs2781521	C9orf57	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71995000-72012600	Weak transcription	Aorta	Aorta
2	chr9:72002800-72012400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:72003400-72012400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:72003400-72012400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:72003600-72026200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:72006200-72013400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr9:72007000-72012800	Weak transcription	Esophagus	oesophagus
8	chr9:72007600-72026800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:72007800-72012400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:72008000-72012600	Weak transcription	HSMMtube	muscle
11	chr9:72008200-72012400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr9:72008400-72012400	Weak transcription	Fetal Muscle Leg	muscle
13	chr9:72008400-72012400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr9:72008600-72012600	Weak transcription	Ovary	ovary
15	chr9:72009000-72024400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr9:72009400-72013200	Enhancers	Brain Hippocampus Middle	brain
17	chr9:72009600-72012400	Enhancers	Brain Anterior Caudate	brain
18	chr9:72009800-72013200	Enhancers	Brain Cingulate Gyrus	brain
19	chr9:72010000-72012400	Weak transcription	Right Ventricle	heart
20	chr9:72010000-72013000	Enhancers	Brain Angular Gyrus	brain
21	chr9:72010000-72027800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:72010400-72012400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:72010600-72012800	Weak transcription	Fetal Heart	heart
24	chr9:72010800-72013000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:72011000-72026800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr9:72011200-72012800	Weak transcription	Fetal Stomach	stomach
27	chr9:72011200-72013000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:72011200-72013200	Enhancers	Brain Substantia Nigra	brain
29	chr9:72011800-72012400	Enhancers	Stomach Smooth Muscle	stomach
30	chr9:72011800-72013200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:72012000-72012800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr9:72012000-72013200	Enhancers	Colon Smooth Muscle	Colon
33	chr9:72012000-72013200	Enhancers	Left Ventricle	heart
34	chr9:72012200-72012400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr9:72012200-72012400	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr9:72012200-72012600	Weak transcription	Right Atrium	heart
37	chr9:72012200-72012800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:72012200-72012800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:72012200-72012800	Enhancers	Adipose Nuclei	Adipose
40	chr9:72012200-72013000	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr9:72012200-72013000	Enhancers	NHEK	skin
42	chr9:72012200-72013200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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