Variant report

Variant	rs2813977
Chromosome Location	chr1:227434376-227434377
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10127638	0.84[CEU][hapmap];0.91[CHB][hapmap];0.86[YRI][hapmap]
rs10495256	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap]
rs12118840	0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1513609	0.84[AFR][1000 genomes]
rs1513617	0.94[ASN][1000 genomes]
rs1849550	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1929855	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs2670470	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2718191	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2718214	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2718220	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2718223	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2813955	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2813956	0.89[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2813957	0.85[EUR][1000 genomes]
rs2953640	0.80[ASW][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap]
rs4146588	0.84[CEU][hapmap]
rs4375224	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4653822	0.83[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6426578	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6426596	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66796195	0.86[ASN][1000 genomes]
rs72753628	0.83[AFR][1000 genomes]
rs72755321	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7531992	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7540155	0.84[CEU][hapmap];0.91[CHB][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7540391	0.89[ASW][hapmap];0.83[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540618	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs938257	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap]

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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:227414200-227453800	Weak transcription	HSMM	muscle
3	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:227420800-227434600	Weak transcription	Spleen	Spleen
5	chr1:227424800-227440800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:227425400-227445200	Weak transcription	Osteobl	bone
7	chr1:227430600-227434600	Enhancers	Fetal Heart	heart
8	chr1:227431600-227435400	Weak transcription	NHLF	lung
9	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
10	chr1:227431800-227439200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:227431800-227443000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:227432000-227434400	Enhancers	Brain Substantia Nigra	brain
13	chr1:227432000-227434800	Enhancers	HepG2	liver
14	chr1:227432000-227435200	Weak transcription	Fetal Brain Female	brain
15	chr1:227432000-227459200	Weak transcription	Fetal Lung	lung
16	chr1:227432200-227455400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:227432400-227434800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:227432400-227434800	Enhancers	HMEC	breast
19	chr1:227432400-227435000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr1:227432600-227434800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:227432600-227435200	Enhancers	Liver	Liver
22	chr1:227432600-227436200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:227432600-227448000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:227432800-227434800	Weak transcription	Fetal Intestine Large	intestine
25	chr1:227432800-227435400	Weak transcription	Fetal Muscle Leg	muscle
26	chr1:227432800-227435600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:227432800-227441600	Weak transcription	Brain Angular Gyrus	brain
28	chr1:227432800-227442400	Weak transcription	K562	blood
29	chr1:227432800-227446000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:227432800-227455600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:227433000-227436600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:227433000-227438000	Weak transcription	Psoas Muscle	Psoas
33	chr1:227433000-227438400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:227433000-227441600	Weak transcription	A549	lung
35	chr1:227433000-227446000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:227433000-227446000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:227433000-227469000	Weak transcription	Aorta	Aorta
38	chr1:227433200-227434400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:227433200-227434600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:227433200-227452800	Weak transcription	Ovary	ovary
41	chr1:227433400-227435000	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr1:227433600-227434600	Enhancers	NHEK	skin
43	chr1:227433800-227434800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:227434000-227434800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr1:227434000-227435600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:227434000-227435800	Weak transcription	Brain Anterior Caudate	brain
47	chr1:227434000-227442200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:227434000-227444200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:227434000-227446800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:227434000-227447000	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links