Variant report

Variant	rs595696
Chromosome Location	chr13:96679916-96679917
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1807900	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1980942	0.81[CEU][hapmap]
rs2389530	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2774113	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs3099359	0.89[CHB][hapmap]
rs34482628	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs472788	0.84[EUR][1000 genomes]
rs473930	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs4773927	0.88[CEU][hapmap];0.94[CHB][hapmap]
rs481927	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs485648	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs489179	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs493109	0.88[CEU][hapmap]
rs506474	0.82[EUR][1000 genomes]
rs509572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs511029	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs517173	0.83[EUR][1000 genomes]
rs521235	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs527096	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs527680	0.89[CEU][hapmap]
rs529306	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs531090	0.82[EUR][1000 genomes]
rs532399	0.82[EUR][1000 genomes]
rs535812	0.85[EUR][1000 genomes]
rs536606	0.82[EUR][1000 genomes]
rs539604	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs541811	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs544080	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs551457	0.84[EUR][1000 genomes]
rs552598	0.83[EUR][1000 genomes]
rs555221	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs561996	0.82[EUR][1000 genomes]
rs566894	0.80[EUR][1000 genomes]
rs576184	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs590758	0.83[EUR][1000 genomes]
rs592205	0.82[EUR][1000 genomes]
rs6492826	0.89[CEU][hapmap]
rs7994626	0.81[CEU][hapmap];0.95[CHB][hapmap]
rs7998903	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs816139	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs9516620	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs9516629	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9525085	0.81[CEU][hapmap]
rs9525091	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9525095	0.81[CEU][hapmap]
rs9525098	0.87[CEU][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1051574	chr13:96550653-96779248	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1040320	chr13:96573646-96790859	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv869471	chr13:96622327-97223956	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs595696	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL
rs595696	UGGT2	cis	Muscle Skeletal	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96613200-96694200	Weak transcription	A549	lung
2	chr13:96660200-96682200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr13:96660800-96684800	Weak transcription	Psoas Muscle	Psoas
4	chr13:96663200-96685400	Weak transcription	HMEC	breast
5	chr13:96664200-96684800	Weak transcription	NHLF	lung
6	chr13:96668600-96704400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr13:96668800-96685400	Weak transcription	Gastric	stomach
8	chr13:96669000-96683200	Weak transcription	Esophagus	oesophagus
9	chr13:96669000-96685800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr13:96669000-96686200	Weak transcription	NHEK	skin
11	chr13:96669200-96686800	Weak transcription	Right Ventricle	heart
12	chr13:96669200-96694000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr13:96669400-96680000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr13:96669400-96685400	Weak transcription	Fetal Kidney	kidney
15	chr13:96669400-96685600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr13:96669400-96685600	Weak transcription	Fetal Brain Female	brain
17	chr13:96669400-96694000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr13:96669400-96704600	Weak transcription	Brain Anterior Caudate	brain
19	chr13:96669600-96686400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr13:96669600-96686400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr13:96669600-96687000	Weak transcription	Adipose Nuclei	Adipose
22	chr13:96669800-96685600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr13:96669800-96686200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr13:96669800-96686400	Weak transcription	Fetal Lung	lung
25	chr13:96670400-96680200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr13:96670400-96685800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr13:96672400-96685600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr13:96672800-96684000	Weak transcription	K562	blood
29	chr13:96673000-96680000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr13:96673000-96685000	Weak transcription	GM12878-XiMat	blood
31	chr13:96673000-96685600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr13:96673000-96698400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr13:96673200-96684600	Weak transcription	Hela-S3	cervix
34	chr13:96673200-96686000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr13:96673200-96686400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr13:96673200-96692800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr13:96673200-96693400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr13:96673400-96686000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr13:96673400-96686000	Weak transcription	Fetal Muscle Leg	muscle
40	chr13:96673400-96686400	Weak transcription	Liver	Liver
41	chr13:96673400-96693000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr13:96673600-96681800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr13:96673600-96685400	Weak transcription	Pancreas	Pancrea
44	chr13:96673600-96685600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr13:96673600-96685600	Weak transcription	Fetal Intestine Small	intestine
46	chr13:96673600-96686200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr13:96673600-96686800	Weak transcription	Left Ventricle	heart
48	chr13:96674200-96685800	Weak transcription	Fetal Intestine Large	intestine
49	chr13:96675400-96681600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr13:96676800-96683600	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links