Variant report

Variant	rs11716487
Chromosome Location	chr3:52477866-52477867
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52467987..52470484-chr3:52476648..52478461,2	K562	blood:
2	chr3:52310738..52313208-chr3:52476812..52479185,3	K562	blood:
3	chr3:52310738..52312767-chr3:52476812..52478941,2	K562	blood:

Variant related genes	Relation type
ENSG00000164091	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10460962	1.00[CEU][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs10461027	1.00[CEU][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs1077142	0.86[LWK][hapmap]
rs10865971	1.00[CEU][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs11706515	1.00[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs11707056	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs11708581	0.91[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs11708811	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs11710014	1.00[CEU][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs11711974	1.00[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs11713914	1.00[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs11715391	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs11717028	0.81[EUR][1000 genomes]
rs11717383	0.82[LWK][hapmap]
rs11720365	1.00[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs11721277	0.83[EUR][1000 genomes]
rs13091545	0.86[LWK][hapmap]
rs17052051	1.00[CEU][hapmap]
rs17052052	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs17052053	0.91[CEU][hapmap];0.84[TSI][hapmap]
rs17052054	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs17263770	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1767	0.91[CEU][hapmap]
rs1769	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs35860312	0.86[LWK][hapmap]
rs3733063	0.91[CEU][hapmap];0.84[TSI][hapmap]
rs3886875	1.00[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs498946	0.83[LWK][hapmap]
rs55806905	0.83[EUR][1000 genomes]
rs55813842	0.83[EUR][1000 genomes]
rs56002041	0.83[EUR][1000 genomes]
rs56322342	0.83[EUR][1000 genomes]
rs56899118	0.83[EUR][1000 genomes]
rs57849650	0.83[EUR][1000 genomes]
rs6445385	1.00[CEU][hapmap]
rs648514	0.82[YRI][hapmap]
rs6776759	0.85[EUR][1000 genomes]
rs6793317	0.91[CEU][hapmap];0.84[TSI][hapmap]
rs724801	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs729555	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs73072990	0.89[EUR][1000 genomes]
rs73091166	0.83[EUR][1000 genomes]
rs73091168	0.83[EUR][1000 genomes]
rs746239	0.83[EUR][1000 genomes]
rs7615405	0.81[EUR][1000 genomes]
rs7633687	1.00[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs7638204	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs7643570	0.86[LWK][hapmap]
rs7643913	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv590303	chr3:52469785-52478428	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11716487	DNAH1	cis	parietal	SCAN
rs11716487	SEMA3G	cis	cerebellum	SCAN
rs11716487	DNAH1	cis	cerebellum	SCAN
rs11716487	NISCH	cis	parietal	SCAN
rs11716487	LOC286359	trans	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52450200-52478400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:52469000-52478200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:52470800-52484200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:52471400-52478000	Weak transcription	Right Atrium	heart
5	chr3:52472200-52478200	Weak transcription	Gastric	stomach
6	chr3:52472200-52478600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:52472600-52478000	Weak transcription	Esophagus	oesophagus
8	chr3:52472600-52478400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:52475200-52478400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:52475800-52478800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:52476200-52479400	Active TSS	Brain Anterior Caudate	brain
12	chr3:52476400-52478600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:52476600-52478200	Active TSS	Right Ventricle	heart
14	chr3:52476600-52479600	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr3:52476800-52478000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:52476800-52478200	Active TSS	Spleen	Spleen
17	chr3:52476800-52478400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:52476800-52478600	Active TSS	Stomach Smooth Muscle	stomach
19	chr3:52476800-52479200	Active TSS	Left Ventricle	heart
20	chr3:52476800-52479600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr3:52477000-52478000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
22	chr3:52477200-52478000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr3:52477200-52478400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr3:52477200-52478400	Weak transcription	Colonic Mucosa	Colon
25	chr3:52477200-52479200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:52477200-52479200	Flanking Active TSS	Placenta	Placenta
27	chr3:52477400-52479000	Active TSS	Brain Hippocampus Middle	brain
28	chr3:52477400-52479000	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr3:52477400-52479000	Flanking Active TSS	Fetal Muscle Leg	muscle
30	chr3:52477600-52478200	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr3:52477600-52478400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr3:52477600-52478400	Active TSS	Lung	lung
33	chr3:52477600-52478400	Enhancers	HUVEC	blood vessel
34	chr3:52477600-52479200	Active TSS	Psoas Muscle	Psoas
35	chr3:52477800-52478200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:52477800-52478400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:52477800-52478400	Active TSS	Pancreas	Pancrea
38	chr3:52477800-52478800	Flanking Active TSS	HepG2	liver
39	chr3:52477800-52480800	Weak transcription	Brain Cingulate Gyrus	brain

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