Variant report

Variant	rs2290108
Chromosome Location	chr2:114470778-114470779
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	chr2:114470204..114472162-chr2:114473968..114476714,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10167730	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs10172842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10177576	0.90[EUR][1000 genomes]
rs10179657	0.90[EUR][1000 genomes]
rs10209098	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1375332	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2122097	0.88[EUR][1000 genomes]
rs2305255	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2442136	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs2595152	0.94[CEU][hapmap]
rs2687627	0.85[EUR][1000 genomes]
rs28451366	0.88[EUR][1000 genomes]
rs2900744	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36062527	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3816384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3890789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4848343	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4848345	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4849270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4849277	0.84[EUR][1000 genomes]
rs4849279	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs6711542	0.85[EUR][1000 genomes]
rs7560480	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7577893	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7600228	0.95[CEU][hapmap];0.87[EUR][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2290108	SLC35F5	Cis_1M	lymphoblastoid	RTeQTL
rs2290108	RPL23AP7	cis	Esophagus Muscularis	GTEx
rs2290108	RPL23AP7	cis	lung	GTEx
rs2290108	RPL23AP7	cis	Nerve Tibial	GTEx
rs2290108	RPL23AP7	cis	Muscle Skeletal	GTEx
rs2290108	RPL23AP7	cis	Whole Blood	GTEx
rs2290108	DDX11L2	cis	Whole Blood	GTEx
rs2290108	RPL23AP7	cis	Artery Aorta	GTEx
rs2290108	RPL23AP7	cis	Artery Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114455400-114472200	Weak transcription	HMEC	breast
2	chr2:114458000-114472000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr2:114458200-114486200	Weak transcription	Dnd41	blood
4	chr2:114458200-114512600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:114458400-114471800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr2:114458400-114475000	Weak transcription	Thymus	Thymus
7	chr2:114458400-114484200	Weak transcription	Pancreas	Pancrea
8	chr2:114458400-114497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:114458400-114500000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:114460200-114484200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:114460800-114475200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:114461000-114472600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:114461200-114473200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:114461400-114472200	Weak transcription	A549	lung
15	chr2:114461400-114513200	Weak transcription	Small Intestine	intestine
16	chr2:114461600-114484200	Weak transcription	Lung	lung
17	chr2:114461600-114484400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:114461600-114499800	Weak transcription	Hela-S3	cervix
19	chr2:114461800-114472400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:114462000-114497400	Weak transcription	Colonic Mucosa	Colon
21	chr2:114463000-114498800	Weak transcription	Esophagus	oesophagus
22	chr2:114463800-114473000	Weak transcription	Brain Hippocampus Middle	brain
23	chr2:114464000-114473800	Weak transcription	Brain Anterior Caudate	brain
24	chr2:114464000-114473800	Weak transcription	Psoas Muscle	Psoas
25	chr2:114464000-114484200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:114464000-114484200	Weak transcription	Gastric	stomach
27	chr2:114464000-114497600	Weak transcription	Right Ventricle	heart
28	chr2:114464000-114497600	Weak transcription	Spleen	Spleen
29	chr2:114464400-114473000	Weak transcription	Fetal Lung	lung
30	chr2:114464600-114484600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr2:114465000-114472000	Weak transcription	HepG2	liver
32	chr2:114465200-114486400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:114465200-114512000	Weak transcription	Stomach Mucosa	stomach
34	chr2:114465800-114480000	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:114465800-114484800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:114466200-114470800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:114466200-114473800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:114466800-114474600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:114466800-114475400	Weak transcription	Brain Germinal Matrix	brain
40	chr2:114467400-114479800	Weak transcription	Brain Angular Gyrus	brain
41	chr2:114467400-114497200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:114467600-114486200	Weak transcription	Fetal Brain Male	brain
43	chr2:114467800-114484200	Weak transcription	Aorta	Aorta
44	chr2:114468400-114475600	Weak transcription	Fetal Intestine Small	intestine
45	chr2:114468600-114474000	Weak transcription	Brain Substantia Nigra	brain
46	chr2:114468800-114512800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr2:114469000-114471200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr2:114469000-114473800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:114469400-114470800	Strong transcription	Left Ventricle	heart
50	chr2:114469400-114471000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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