Variant report

Variant	rs2945960
Chromosome Location	chr19:36977442-36977443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36977340..36979938-chr19:37058785..37061352,2	K562	blood:
2	chr19:36977221..36979834-chr19:36983552..36985787,2	K562	blood:
3	chr19:36867662..36870599-chr19:36976598..36980024,4	K562	blood:
4	chr19:36868112..36870123-chr19:36976598..36979565,2	K562	blood:

Variant related genes	Relation type
ENSG00000142065	Chromatin interaction
ENSG00000266973	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs2052730	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385796	0.81[ASN][1000 genomes]
rs2912420	0.81[ASN][1000 genomes]
rs2912422	0.87[ASN][1000 genomes]
rs2912424	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2912426	0.93[ASN][1000 genomes]
rs2912428	0.91[ASN][1000 genomes]
rs2912431	0.91[ASN][1000 genomes]
rs2912434	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2912436	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2912437	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2945946	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945965	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2945966	0.81[ASN][1000 genomes]
rs2945967	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2945968	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2945970	0.92[ASN][1000 genomes]
rs2945974	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2945977	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2945979	0.85[ASN][1000 genomes]
rs2945982	0.92[ASN][1000 genomes]
rs2945988	0.86[ASN][1000 genomes]
rs2967432	0.84[ASN][1000 genomes]
rs2967441	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2967448	0.83[ASN][1000 genomes]
rs2967449	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2967450	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2967451	0.86[ASN][1000 genomes]
rs2967452	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2967456	0.93[ASN][1000 genomes]
rs2967457	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967462	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2967467	0.81[ASN][1000 genomes]
rs2967471	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2967474	0.93[ASN][1000 genomes]
rs2967475	0.85[ASN][1000 genomes]
rs2967505	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2967542	0.87[ASN][1000 genomes]
rs2967544	0.93[ASN][1000 genomes]
rs3107238	0.81[ASN][1000 genomes]
rs3111554	0.86[ASN][1000 genomes]
rs4561584	0.86[ASN][1000 genomes]

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	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv911648	chr19:36914171-37047472	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv1067364	chr19:36921204-36985874	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36936400-36978400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:36941000-36979000	Weak transcription	Hela-S3	cervix
3	chr19:36945800-36979000	Weak transcription	Fetal Heart	heart
4	chr19:36957200-36979600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:36957400-36979400	Weak transcription	NH-A	brain
6	chr19:36960400-36979600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:36963400-36979200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr19:36964000-36979800	Weak transcription	Esophagus	oesophagus
9	chr19:36964200-36978200	Weak transcription	Brain Angular Gyrus	brain
10	chr19:36964200-36979000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr19:36964200-36979000	Weak transcription	Osteobl	bone
12	chr19:36964200-36979200	Weak transcription	Stomach Mucosa	stomach
13	chr19:36964200-36979400	Weak transcription	Brain Anterior Caudate	brain
14	chr19:36964200-36979600	Weak transcription	Placenta	Placenta
15	chr19:36964200-36979600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr19:36964400-36978800	Weak transcription	K562	blood
17	chr19:36964400-36979000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:36964600-36979200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr19:36964600-36979400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr19:36964800-36979600	Weak transcription	Fetal Kidney	kidney
21	chr19:36965400-36979200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:36965800-36978000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr19:36966400-36978400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:36966400-36979000	Weak transcription	Colon Smooth Muscle	Colon
25	chr19:36966400-36979200	Weak transcription	Adipose Nuclei	Adipose
26	chr19:36966400-36979600	Weak transcription	HSMMtube	muscle
27	chr19:36966600-36978200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr19:36966600-36979000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:36966600-36979000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:36966600-36979000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:36966600-36979400	Weak transcription	Right Ventricle	heart
32	chr19:36967800-36979000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:36967800-36979600	Weak transcription	Left Ventricle	heart
34	chr19:36970000-36978000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr19:36970000-36979000	Weak transcription	Pancreas	Pancrea
36	chr19:36970000-36979200	Weak transcription	HSMM	muscle
37	chr19:36970000-36979600	Weak transcription	Psoas Muscle	Psoas
38	chr19:36970000-36979600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:36970600-36979000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:36970800-36979800	Weak transcription	Spleen	Spleen
41	chr19:36971800-36979000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:36973200-36977600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:36973200-36979200	Weak transcription	NHEK	skin
44	chr19:36973800-36979400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:36974200-36978200	Weak transcription	Brain Hippocampus Middle	brain
46	chr19:36974400-36978200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr19:36974400-36979200	Weak transcription	Brain Substantia Nigra	brain
48	chr19:36974400-36979400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:36974400-36979600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:36974800-36978200	ZNF genes & repeats	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links