Variant report

Variant	rs2890358
Chromosome Location	chr1:10027540-10027541
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10779734	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11121510	0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11121512	0.91[ASN][1000 genomes]
rs11828	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12140009	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12140015	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12140058	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1220389	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1220397	0.85[ASN][1000 genomes]
rs1220398	0.87[CHB][hapmap];0.90[CHD][hapmap]
rs1220399	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1220400	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1220402	0.91[ASN][1000 genomes]
rs1220420	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1220421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1220424	0.91[ASN][1000 genomes]
rs1234694	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1628143	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1660733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2919694	0.87[ASN][1000 genomes]
rs3003376	0.93[ASW][hapmap];0.92[CEU][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3003377	0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3003378	0.87[ASW][hapmap];0.85[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3013783	0.87[ASN][1000 genomes]
rs3013784	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3013788	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3123522	0.92[CEU][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3762290	0.85[LWK][hapmap];0.84[MKK][hapmap]
rs6541073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661806	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6664631	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6671289	0.83[MKK][hapmap]
rs6678023	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6680076	0.86[ASN][1000 genomes]
rs7517360	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7517806	0.84[ASN][1000 genomes]
rs7517812	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7528979	0.81[ASW][hapmap];0.86[CHD][hapmap];0.92[LWK][hapmap];0.88[MKK][hapmap]
rs7539191	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv1005461	chr1:9972921-10038862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
9	nsv534855	chr1:9972921-10038862	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2890358	MTHFR	cis	cerebellum	SCAN
rs2890358	LZIC	cis	lymphoblastoid	seeQTL
rs2890358	LZIC	cis	multi-tissue	Pritchard
rs2890358	LZIC	Cis_1M	lymphoblastoid	RTeQTL
rs2890358	HES3	cis	cerebellum	SCAN
rs2890358	LZIC	cis	Lymphoblastoid	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10004000-10034000	Weak transcription	Aorta	Aorta
2	chr1:10004200-10033800	Weak transcription	Gastric	stomach
3	chr1:10004400-10031600	Weak transcription	Fetal Intestine Large	intestine
4	chr1:10004600-10032400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:10004800-10031600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:10004800-10032200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:10004800-10032400	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:10008000-10031800	Weak transcription	Lung	lung
9	chr1:10008000-10032000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:10008000-10032200	Weak transcription	Colonic Mucosa	Colon
11	chr1:10008000-10035000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:10008200-10032000	Weak transcription	Liver	Liver
13	chr1:10008200-10032200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:10008400-10031800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:10008400-10032000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:10008400-10032200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:10008600-10031800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:10008600-10033200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:10008600-10035600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:10010800-10032000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:10010800-10032000	Weak transcription	Thymus	Thymus
22	chr1:10010800-10032200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:10010800-10032600	Weak transcription	Primary T cells from cord blood	blood
24	chr1:10010800-10034800	Weak transcription	NHEK	skin
25	chr1:10010800-10035000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:10010800-10035600	Weak transcription	Fetal Kidney	kidney
27	chr1:10010800-10036400	Weak transcription	Esophagus	oesophagus
28	chr1:10011000-10031800	Weak transcription	Left Ventricle	heart
29	chr1:10011000-10031800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:10011000-10032200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:10011000-10032200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:10011000-10032400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr1:10011000-10032600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:10011000-10032600	Weak transcription	Fetal Thymus	thymus
35	chr1:10011000-10034200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:10011000-10044800	Weak transcription	NHDF-Ad	bronchial
37	chr1:10011200-10031600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:10011200-10032200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:10011200-10032400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:10011400-10027800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:10011400-10032000	Weak transcription	Adipose Nuclei	Adipose
42	chr1:10011400-10032600	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:10011600-10032200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:10011800-10031800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:10011800-10032000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:10011800-10032200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:10011800-10032400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:10011800-10042200	Weak transcription	K562	blood
49	chr1:10012000-10032400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:10013000-10031600	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links