Variant report

Variant	rs2166965
Chromosome Location	chr2:114474911-114474912
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	chr2:114473851..114476041-chr2:114476528..114479274,2	K562	blood:
2	chr2:114470204..114472162-chr2:114473968..114476714,2	K562	blood:

Variant related genes	Relation type
ENSG00000265429	Chromatin interaction
ENSG00000115084	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10514810	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs11674510	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11676758	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677881	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.92[ASN][1000 genomes]
rs11679736	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11684486	0.90[AFR][1000 genomes]
rs11685171	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11687572	0.97[ASN][1000 genomes]
rs11694541	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17632073	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17633527	0.93[ASN][1000 genomes]
rs17683666	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17684620	0.92[ASN][1000 genomes]
rs2290107	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748907	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41377545	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.97[ASN][1000 genomes]
rs4849271	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58351064	0.92[ASN][1000 genomes]
rs6708711	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.97[ASN][1000 genomes]
rs6709158	0.82[CHB][hapmap]
rs6725990	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6726001	0.82[CHB][hapmap]
rs6732182	0.95[ASN][1000 genomes]
rs73955055	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73955056	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73955057	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73955059	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73955070	0.92[ASN][1000 genomes]
rs7581858	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7599741	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7599832	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9753198	0.95[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001195	chr2:114362003-114506330	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv979109	chr2:114429638-114495192	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv979339	chr2:114430138-114495192	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2166965	DDX11L2	cis	Whole Blood	GTEx
rs2166965	DDX11L2	cis	lung	GTEx
rs2166965	DDX11L2	cis	Esophagus Mucosa	GTEx
rs2166965	DDX11L2	cis	Nerve Tibial	GTEx
rs2166965	CHCHD5	cis	cerebellum	SCAN
rs2166965	RPL23AP7	cis	Artery Tibial	GTEx
rs2166965	DDX11L2	cis	Artery Tibial	GTEx
rs2166965	IL1A	cis	lymphoblastoid	seeQTL
rs2166965	RPL23AP7	cis	Whole Blood	GTEx
rs2166965	RPL23AP7	cis	Heart Left Ventricle	GTEx
rs2166965	RPL23AP7	Cis_1M	lymphoblastoid	RTeQTL
rs2166965	DDX11L2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114458200-114486200	Weak transcription	Dnd41	blood
2	chr2:114458200-114512600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:114458400-114475000	Weak transcription	Thymus	Thymus
4	chr2:114458400-114484200	Weak transcription	Pancreas	Pancrea
5	chr2:114458400-114497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:114458400-114500000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:114460200-114484200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:114460800-114475200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:114461400-114513200	Weak transcription	Small Intestine	intestine
10	chr2:114461600-114484200	Weak transcription	Lung	lung
11	chr2:114461600-114484400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:114461600-114499800	Weak transcription	Hela-S3	cervix
13	chr2:114462000-114497400	Weak transcription	Colonic Mucosa	Colon
14	chr2:114463000-114498800	Weak transcription	Esophagus	oesophagus
15	chr2:114464000-114484200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:114464000-114484200	Weak transcription	Gastric	stomach
17	chr2:114464000-114497600	Weak transcription	Right Ventricle	heart
18	chr2:114464000-114497600	Weak transcription	Spleen	Spleen
19	chr2:114464600-114484600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:114465200-114486400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:114465200-114512000	Weak transcription	Stomach Mucosa	stomach
22	chr2:114465800-114480000	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:114465800-114484800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:114466800-114475400	Weak transcription	Brain Germinal Matrix	brain
25	chr2:114467400-114479800	Weak transcription	Brain Angular Gyrus	brain
26	chr2:114467400-114497200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:114467600-114486200	Weak transcription	Fetal Brain Male	brain
28	chr2:114467800-114484200	Weak transcription	Aorta	Aorta
29	chr2:114468400-114475600	Weak transcription	Fetal Intestine Small	intestine
30	chr2:114468800-114512800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr2:114469400-114477200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:114469400-114477200	Strong transcription	Placenta	Placenta
33	chr2:114469400-114477400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:114469400-114510400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr2:114469600-114476800	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr2:114469800-114482000	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr2:114469800-114486400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr2:114470000-114477400	Strong transcription	Primary B cells from cord blood	blood
39	chr2:114470000-114497400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:114470000-114500200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:114470200-114475800	Strong transcription	Primary hematopoietic stem cells	blood
42	chr2:114470200-114477200	Strong transcription	Liver	Liver
43	chr2:114470200-114477400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr2:114470200-114477400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:114470200-114493400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:114470200-114511200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr2:114470400-114475200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr2:114470400-114477000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr2:114470400-114477200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:114470400-114477400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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