Variant report

Variant	rs39949
Chromosome Location	chr5:50108245-50108246
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10035164	0.88[ASN][1000 genomes]
rs10036060	0.88[ASN][1000 genomes]
rs10039272	0.80[ASN][1000 genomes]
rs10043477	0.80[EUR][1000 genomes]
rs10044566	0.88[ASN][1000 genomes]
rs10051561	0.80[ASN][1000 genomes]
rs10054381	0.88[ASN][1000 genomes]
rs10056836	0.88[ASN][1000 genomes]
rs10059085	0.80[ASN][1000 genomes]
rs10060850	0.88[ASN][1000 genomes]
rs10065432	0.80[ASN][1000 genomes]
rs10072398	0.80[ASN][1000 genomes]
rs10075034	0.88[ASN][1000 genomes]
rs10085036	0.88[ASN][1000 genomes]
rs10471956	0.83[EUR][1000 genomes]
rs10755235	0.83[EUR][1000 genomes]
rs10940472	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10940497	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11739828	0.83[EUR][1000 genomes]
rs11750241	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11750771	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12188262	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12188654	0.81[ASN][1000 genomes]
rs12519006	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12521579	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13153982	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13173734	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13359044	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13361410	0.88[ASN][1000 genomes]
rs1375127	0.83[EUR][1000 genomes]
rs152102	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs154133	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs154134	0.92[ASN][1000 genomes]
rs154135	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs154137	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs154138	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs154140	0.92[ASN][1000 genomes]
rs154141	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs157970	0.87[EUR][1000 genomes]
rs16884018	0.81[ASN][1000 genomes]
rs169497	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs171555	0.90[EUR][1000 genomes]
rs17195388	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs182230	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2548581	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2548582	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2548583	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs256340	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs256341	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2594706	0.85[ASN][1000 genomes]
rs26062	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26065	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs26066	0.90[EUR][1000 genomes]
rs26068	0.90[EUR][1000 genomes]
rs26069	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs26071	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs27156	0.85[EUR][1000 genomes]
rs27244	0.85[EUR][1000 genomes]
rs27245	0.87[EUR][1000 genomes]
rs27251	0.87[EUR][1000 genomes]
rs27254	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27264	0.92[ASN][1000 genomes]
rs27357	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27465	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs27468	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs27469	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs27574	0.85[EUR][1000 genomes]
rs27609	0.82[EUR][1000 genomes]
rs27627	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs27725	0.86[EUR][1000 genomes]
rs28085	0.86[EUR][1000 genomes]
rs282549	0.90[EUR][1000 genomes]
rs282550	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs282551	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs282552	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs282553	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs282557	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs282559	0.85[EUR][1000 genomes]
rs282561	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28505342	0.80[ASN][1000 genomes]
rs28711235	0.80[ASN][1000 genomes]
rs32376	0.92[ASN][1000 genomes]
rs32377	0.90[EUR][1000 genomes]
rs32378	0.90[EUR][1000 genomes]
rs32404	0.88[ASN][1000 genomes]
rs32425	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3763367	0.81[ASN][1000 genomes]
rs39613	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4029420	0.83[EUR][1000 genomes]
rs41502	0.82[EUR][1000 genomes]
rs42284	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4865628	0.85[ASN][1000 genomes]
rs57079776	0.81[ASN][1000 genomes]
rs62366937	0.85[ASN][1000 genomes]
rs6450359	0.83[EUR][1000 genomes]
rs6869356	0.80[EUR][1000 genomes]
rs6872496	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6886872	0.83[EUR][1000 genomes]
rs6890519	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73101075	0.88[ASN][1000 genomes]
rs7728126	0.80[ASN][1000 genomes]
rs895801	0.83[EUR][1000 genomes]
rs921210	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1016237	chr5:49986171-50118816	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv537761	chr5:49986171-50118816	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs39949	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50056800-50126400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:50064000-50126800	Weak transcription	Osteobl	bone
3	chr5:50071600-50138200	Weak transcription	Placenta	Placenta
4	chr5:50078200-50140000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:50083200-50116800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:50085400-50123800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:50085400-50136200	Weak transcription	Thymus	Thymus
8	chr5:50091200-50113800	Weak transcription	Fetal Stomach	stomach
9	chr5:50091200-50116200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:50091200-50118800	Weak transcription	Spleen	Spleen
11	chr5:50091200-50123800	Weak transcription	Fetal Thymus	thymus
12	chr5:50091200-50124800	Weak transcription	Esophagus	oesophagus
13	chr5:50091200-50130400	Weak transcription	Pancreas	Pancrea
14	chr5:50091200-50133600	Weak transcription	Lung	lung
15	chr5:50091200-50136000	Weak transcription	Gastric	stomach
16	chr5:50091200-50140600	Weak transcription	Small Intestine	intestine
17	chr5:50091400-50124000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr5:50091800-50123400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:50093200-50112200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:50094000-50111200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:50094000-50123800	Weak transcription	HMEC	breast
22	chr5:50094200-50111600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:50095800-50114800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:50095800-50123400	Weak transcription	Fetal Lung	lung
25	chr5:50096000-50132200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr5:50099200-50112000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:50099400-50115600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr5:50099400-50123800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:50100000-50118600	Weak transcription	Aorta	Aorta
30	chr5:50100200-50111800	Weak transcription	Liver	Liver
31	chr5:50100200-50112200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr5:50100200-50113200	Weak transcription	GM12878-XiMat	blood
33	chr5:50100200-50116200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr5:50100200-50139400	Weak transcription	Ovary	ovary
35	chr5:50100400-50111600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr5:50100400-50116800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr5:50100400-50118800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr5:50100400-50123800	Weak transcription	Left Ventricle	heart
39	chr5:50101800-50110800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr5:50102000-50113000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr5:50102200-50110400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr5:50102400-50118400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr5:50102600-50111400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr5:50104000-50109600	Weak transcription	Dnd41	blood
45	chr5:50104400-50110400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr5:50104400-50111400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr5:50104600-50109400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:50104600-50110400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:50104600-50111400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr5:50104600-50111800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links