Variant report

Variant	rs673753
Chromosome Location	chr11:65206017-65206018
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65178877..65218546-chr11:65218612..65286191,1014	K562	blood:

Variant related genes	Relation type
ENSG00000270526	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000173727	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11602839	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs11605125	1.00[CEU][hapmap]
rs1194758	0.87[CEU][hapmap]
rs1787666	0.87[CEU][hapmap]
rs2073801	0.85[CEU][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs2904976	0.85[CEU][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs475967	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs481335	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508286	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs512715	0.81[JPT][hapmap]
rs550015	0.85[CEU][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs550894	0.92[EUR][1000 genomes]
rs580933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61154080	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs613316	0.81[JPT][hapmap]
rs616599	0.87[CEU][hapmap]
rs666834	0.85[CEU][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs674485	0.81[JPT][hapmap]
rs686320	0.85[CEU][hapmap]

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	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	esv2422285	chr11:65013294-65254540	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
3	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
4	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
5	nsv541065	chr11:65117387-65271894	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	835 gene(s)	inside rSNPs	diseases
6	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	963 gene(s)	inside rSNPs	diseases
7	nsv897717	chr11:65140209-65278461	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	942 gene(s)	inside rSNPs	diseases
8	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
9	nsv541066	chr11:65142779-65271894	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	833 gene(s)	inside rSNPs	diseases
10	nsv541067	chr11:65142779-65313799	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	950 gene(s)	inside rSNPs	diseases
11	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
12	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
13	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription 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 miRNA target site	972 gene(s)	inside rSNPs	diseases
14	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
15	nsv897719	chr11:65157094-65335705	Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
16	nsv541072	chr11:65171202-65313799	Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	946 gene(s)	inside rSNPs	diseases
17	nsv541073	chr11:65171202-65331136	Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
18	nsv541074	chr11:65171202-65368787	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	961 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs673753	CATSPER1	cis	parietal	SCAN
rs673753	SLC22A25	cis	cerebellum	SCAN
rs673753	SLC22A11	cis	parietal	SCAN
rs673753	PPP6R3	cis	cerebellum	SCAN
rs673753	POLA2	cis	parietal	SCAN
rs673753	PLCB3	cis	cerebellum	SCAN
rs673753	NEAT1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65190600-65206600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr11:65191000-65206800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr11:65193800-65209800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:65197400-65207600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:65197800-65206800	Weak transcription	Fetal Brain Male	brain
6	chr11:65197800-65209200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:65198000-65209400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr11:65198000-65216000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:65198200-65209400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:65198800-65209400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:65199000-65206800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
12	chr11:65200200-65206600	Genic enhancers	HepG2	liver
13	chr11:65200200-65207000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:65200400-65206400	Genic enhancers	Colon Smooth Muscle	Colon
15	chr11:65200400-65206600	Genic enhancers	Brain Hippocampus Middle	brain
16	chr11:65200600-65206800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr11:65200600-65211600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
18	chr11:65200600-65214200	Strong transcription	NH-A	brain
19	chr11:65200800-65206800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:65201400-65206400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr11:65201400-65207400	Genic enhancers	K562	blood
22	chr11:65201400-65209200	Strong transcription	Fetal Muscle Leg	muscle
23	chr11:65201600-65206200	Genic enhancers	Brain Anterior Caudate	brain
24	chr11:65201600-65206600	Strong transcription	Primary hematopoietic stem cells	blood
25	chr11:65201600-65206800	Strong transcription	Primary T cells from cord blood	blood
26	chr11:65201600-65206800	Strong transcription	Fetal Intestine Large	intestine
27	chr11:65201600-65206800	Strong transcription	HSMMtube	muscle
28	chr11:65201600-65207400	Strong transcription	Fetal Thymus	thymus
29	chr11:65201600-65207600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:65201600-65208000	Strong transcription	Fetal Muscle Trunk	muscle
31	chr11:65201600-65208200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:65201600-65211600	Genic enhancers	Brain Substantia Nigra	brain
33	chr11:65201800-65206400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr11:65201800-65206600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr11:65201800-65206600	Genic enhancers	Brain Cingulate Gyrus	brain
36	chr11:65201800-65206600	Strong transcription	Fetal Kidney	kidney
37	chr11:65201800-65208400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr11:65202000-65206800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr11:65202200-65206400	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:65202200-65208400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr11:65202400-65206600	Strong transcription	NHEK	skin
42	chr11:65202600-65206800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:65202600-65206800	Strong transcription	HMEC	breast
44	chr11:65202600-65214400	Genic enhancers	A549	lung
45	chr11:65203200-65206800	Genic enhancers	Primary monocytes fromperipheralblood	blood
46	chr11:65203200-65211600	Strong transcription	HUVEC	blood vessel
47	chr11:65203400-65207000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr11:65203400-65212200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr11:65203600-65207000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr11:65203800-65206600	Strong transcription	Fetal Lung	lung

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