Variant report

Variant	rs11143741
Chromosome Location	chr9:71409931-71409932
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71398863..71402159-chr9:71407140..71410574,3	K562	blood:
2	chr9:71394580..71396149-chr9:71409083..71412062,2	K562	blood:
3	chr9:71390215..71393175-chr9:71408433..71409952,2	K562	blood:
4	chr9:71403930..71406409-chr9:71407791..71410873,3	MCF-7	breast:
5	chr9:71408861..71411177-chr9:71411346..71415020,3	K562	blood:

Variant related genes	Relation type
ENSG00000187866	Chromatin interaction
ENSG00000236998	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10448338	0.93[CEU][hapmap]
rs10869320	0.88[CEU][hapmap]
rs10869538	0.81[CEU][hapmap]
rs11143608	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143691	0.94[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143693	1.00[JPT][hapmap]
rs11143697	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143715	0.85[EUR][1000 genomes]
rs11143731	1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143761	0.87[CEU][hapmap]
rs11143777	0.88[CEU][hapmap]
rs11143882	0.88[CEU][hapmap]
rs11143951	0.87[CEU][hapmap]
rs11143988	0.81[CEU][hapmap]
rs11144027	1.00[ASN][1000 genomes]
rs11144074	0.86[CEU][hapmap]
rs11144136	0.87[CEU][hapmap]
rs11144138	0.86[CEU][hapmap]
rs11144152	0.88[CEU][hapmap]
rs11144154	0.87[CEU][hapmap]
rs11144163	0.87[CEU][hapmap]
rs11144178	0.87[CEU][hapmap]
rs11144181	0.87[CEU][hapmap]
rs11144206	0.81[CEU][hapmap]
rs11144215	0.87[CEU][hapmap]
rs11144305	0.87[CEU][hapmap]
rs11144351	0.86[CEU][hapmap]
rs12000088	1.00[ASN][1000 genomes]
rs12003432	0.81[CEU][hapmap]
rs12339235	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs12376037	0.88[CEU][hapmap]
rs12376991	0.87[CEU][hapmap]
rs12377033	0.88[CEU][hapmap]
rs12379061	0.88[CEU][hapmap]
rs12552102	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12555728	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412987	1.00[ASN][1000 genomes]
rs1414951	0.88[CEU][hapmap]
rs1414954	0.87[CEU][hapmap]
rs17057680	0.81[CEU][hapmap]
rs17058780	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs17391456	0.87[CEU][hapmap]
rs17391582	0.87[CEU][hapmap]
rs17483165	0.88[CEU][hapmap]
rs4623507	0.93[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62552125	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62552126	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62552127	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62552128	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62552130	1.00[ASN][1000 genomes]
rs62552131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717924	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs950786	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv1050741	chr9:71405224-71450033	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv540148	chr9:71405224-71450033	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71397200-71417400	Weak transcription	Lung	lung
2	chr9:71399000-71420200	Weak transcription	Fetal Stomach	stomach
3	chr9:71399800-71413200	Weak transcription	Dnd41	blood
4	chr9:71402600-71413400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:71402600-71413600	Weak transcription	Primary T cells from cord blood	blood
6	chr9:71403200-71419800	Weak transcription	Pancreas	Pancrea
7	chr9:71404600-71431400	Weak transcription	HepG2	liver
8	chr9:71404800-71413200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr9:71408000-71410200	Enhancers	Gastric	stomach
10	chr9:71408000-71410200	Enhancers	K562	blood
11	chr9:71408200-71410400	Enhancers	Fetal Intestine Small	intestine
12	chr9:71408400-71410200	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr9:71408800-71410200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr9:71408800-71410400	Enhancers	Fetal Intestine Large	intestine
15	chr9:71409000-71410000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:71409000-71410200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr9:71409000-71410200	Enhancers	Adipose Nuclei	Adipose
18	chr9:71409000-71413400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr9:71409000-71417400	Weak transcription	Right Atrium	heart
20	chr9:71409200-71410000	Weak transcription	Right Ventricle	heart
21	chr9:71409200-71410200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:71409200-71413200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:71409200-71413400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr9:71409200-71421000	Weak transcription	Placenta	Placenta
25	chr9:71409600-71410200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr9:71409600-71410200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:71409600-71410200	Enhancers	Small Intestine	intestine
28	chr9:71409600-71410400	Enhancers	Stomach Mucosa	stomach
29	chr9:71409600-71412000	Weak transcription	Primary B cells from cord blood	blood
30	chr9:71409600-71412000	Weak transcription	Primary B cells from peripheral blood	blood
31	chr9:71409800-71410000	Enhancers	Duodenum Mucosa	Duodenum
32	chr9:71409800-71410000	Enhancers	Left Ventricle	heart
33	chr9:71409800-71410000	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr9:71409800-71410200	Enhancers	H9 Cell Line	embryonic stem cell
35	chr9:71409800-71410200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:71409800-71410200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr9:71409800-71410200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr9:71409800-71410200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr9:71409800-71410200	Enhancers	Aorta	Aorta
40	chr9:71409800-71410200	Flanking Active TSS	Fetal Heart	heart
41	chr9:71409800-71410200	Enhancers	Fetal Lung	lung
42	chr9:71409800-71410600	Enhancers	Fetal Kidney	kidney
43	chr9:71409800-71413400	Weak transcription	GM12878-XiMat	blood

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