Variant report

Variant	rs41271
Chromosome Location	chr5:115629354-115629355
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10042177	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10051072	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10051302	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10056823	1.00[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10062347	0.82[EUR][1000 genomes]
rs10063312	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs10063392	0.82[EUR][1000 genomes]
rs10066081	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10073458	0.83[EUR][1000 genomes]
rs10075063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10077013	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10078121	0.91[CHB][hapmap]
rs10079176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10079466	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10079691	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1090077	0.88[EUR][1000 genomes]
rs1090078	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11241372	0.83[EUR][1000 genomes]
rs11241374	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs11241375	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs11742938	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11953135	0.83[EUR][1000 genomes]
rs11960815	0.83[EUR][1000 genomes]
rs12054994	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12109104	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12657249	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs13159102	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs13161146	0.83[EUR][1000 genomes]
rs13161987	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs13162293	0.82[EUR][1000 genomes]
rs13172482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1382343	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1382344	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1396478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1396481	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1396482	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs149131	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1508875	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs153588	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs153593	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs153594	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1567335	0.87[CEU][hapmap];0.88[YRI][hapmap]
rs1588267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1644268	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1677405	1.00[CEU][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1677406	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs173813	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs173834	0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs185263	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs253950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs253951	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs253952	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs253955	0.80[AMR][1000 genomes]
rs253959	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs254150	0.83[CHB][hapmap]
rs254151	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs254152	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs254171	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs254172	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs254173	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs254174	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs27125	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs27126	0.85[ASN][1000 genomes]
rs37180	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40192	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42959	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55783029	0.83[EUR][1000 genomes]
rs6594938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6594948	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6861437	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6876901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs712561	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs712574	0.81[ASN][1000 genomes]
rs712579	0.81[ASN][1000 genomes]
rs712588	0.81[ASN][1000 genomes]
rs712591	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs712592	0.81[ASN][1000 genomes]
rs712593	0.81[ASN][1000 genomes]
rs712594	0.81[ASN][1000 genomes]
rs712595	0.81[ASN][1000 genomes]
rs712596	0.81[ASN][1000 genomes]
rs712597	0.81[ASN][1000 genomes]
rs712598	0.81[ASN][1000 genomes]
rs712599	0.81[ASN][1000 genomes]
rs712600	0.81[ASN][1000 genomes]
rs712601	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7723358	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs7732346	0.82[EUR][1000 genomes]
rs7735539	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs784479	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs784481	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs785367	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs785369	0.81[ASN][1000 genomes]
rs785370	0.81[ASN][1000 genomes]
rs785373	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs785374	0.81[ASN][1000 genomes]
rs785375	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs785377	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs803967	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs809188	0.88[EUR][1000 genomes]
rs809210	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs810742	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9326987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv882743	chr5:115501792-115634127	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv882746	chr5:115566026-115704566	Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv882747	chr5:115566636-115662510	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2755740	chr5:115576139-115633474	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1017983	chr5:115578765-115713688	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv2757134	chr5:115578810-115633474	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv2759372	chr5:115578810-115633474	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv2760969	chr5:115583627-115630890	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv882748	chr5:115584159-115669950	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1020633	chr5:115596277-115629523	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1023495	chr5:115596277-115629769	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv2752575	chr5:115596277-115633474	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv1018649	chr5:115596350-115629523	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv1015300	chr5:115597953-115629523	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1028664	chr5:115601522-115630878	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv1034438	chr5:115612225-115630878	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41271	COMMD10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115612800-115633200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:115612800-115633200	Weak transcription	Ovary	ovary
3	chr5:115613400-115641600	Weak transcription	HSMM	muscle
4	chr5:115613600-115632000	Weak transcription	Fetal Heart	heart
5	chr5:115613600-115633000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:115624200-115631800	Weak transcription	Liver	Liver
7	chr5:115624400-115631800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:115624400-115633200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:115624400-115633600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:115625600-115632200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:115625600-115633200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr5:115625600-115633200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr5:115625600-115633200	Weak transcription	Psoas Muscle	Psoas
14	chr5:115625600-115633600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:115625600-115633800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:115625600-115634000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:115625600-115639200	Weak transcription	Fetal Stomach	stomach
18	chr5:115625600-115643000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr5:115625800-115630800	Weak transcription	Fetal Intestine Large	intestine
20	chr5:115625800-115631000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr5:115626000-115633200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:115626000-115633200	Weak transcription	Left Ventricle	heart
23	chr5:115626200-115632000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:115626400-115633400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:115626400-115633800	Weak transcription	Brain Hippocampus Middle	brain
26	chr5:115626600-115633600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr5:115626600-115641600	Weak transcription	Fetal Brain Male	brain
28	chr5:115626800-115642200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr5:115627000-115629400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr5:115627000-115632000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr5:115627000-115633400	Weak transcription	Fetal Lung	lung
32	chr5:115627000-115633800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:115627200-115632200	Weak transcription	Adipose Nuclei	Adipose
34	chr5:115627200-115635200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:115627400-115633600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:115627600-115630200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:115627800-115629600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr5:115627800-115629800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr5:115627800-115630000	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr5:115627800-115630000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr5:115627800-115633200	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr5:115627800-115639200	Weak transcription	Placenta	Placenta
43	chr5:115628000-115629600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr5:115628000-115629800	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr5:115628000-115630400	Strong transcription	Primary B cells from cord blood	blood
46	chr5:115628000-115643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:115628200-115629600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr5:115628400-115632000	Weak transcription	Primary T cells from cord blood	blood
49	chr5:115628400-115633400	Weak transcription	Fetal Kidney	kidney
50	chr5:115628400-115639200	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links