Variant report

Variant	rs2200841
Chromosome Location	chr4:143276611-143276612
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10021260	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10428305	0.84[GIH][hapmap];0.83[JPT][hapmap]
rs1120454	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723890	0.89[GIH][hapmap]
rs12499068	0.92[CEU][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap]
rs12640900	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1353624	0.84[GIH][hapmap]
rs1391092	1.00[CEU][hapmap]
rs1497393	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1497396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1565307	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17016001	0.86[GIH][hapmap]
rs17658809	0.96[CEU][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap]
rs28435783	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28707318	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6827918	0.86[GIH][hapmap]
rs6842192	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7666932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9308149	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931420	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830099	chr4:143138257-143285055	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143265800-143280600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr4:143268400-143283200	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr4:143269400-143278600	Enhancers	Fetal Heart	heart
4	chr4:143270800-143284000	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr4:143271000-143277200	Enhancers	Fetal Lung	lung
6	chr4:143271200-143276800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr4:143272000-143277000	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr4:143272400-143278200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr4:143272400-143279800	Weak transcription	Right Ventricle	heart
10	chr4:143273200-143276800	Weak transcription	Brain Hippocampus Middle	brain
11	chr4:143273400-143276800	Enhancers	HSMM	muscle
12	chr4:143273400-143299000	Weak transcription	Left Ventricle	heart
13	chr4:143273600-143277000	Enhancers	Primary hematopoietic stem cells	blood
14	chr4:143273600-143277000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:143273800-143276800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:143273800-143277000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr4:143273800-143278600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:143274000-143276800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:143274000-143276800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr4:143274000-143277000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:143274000-143277000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:143274000-143278400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr4:143274000-143278800	Enhancers	Dnd41	blood
24	chr4:143274200-143276800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:143274200-143276800	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr4:143274400-143277000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:143274400-143278600	Enhancers	Primary T cells fromperipheralblood	blood
28	chr4:143274400-143281400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:143274600-143277600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr4:143274800-143277000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:143274800-143285800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr4:143274800-143286200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:143274800-143288800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr4:143275200-143277000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:143275200-143277800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr4:143275200-143286000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr4:143275400-143285000	Weak transcription	A549	lung
38	chr4:143275400-143288000	Weak transcription	Aorta	Aorta
39	chr4:143275600-143277000	Weak transcription	NH-A	brain
40	chr4:143275600-143286200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr4:143275800-143277000	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr4:143276000-143276800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr4:143276000-143276800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr4:143276000-143277000	Enhancers	Fetal Intestine Large	intestine
45	chr4:143276000-143277000	Enhancers	Fetal Intestine Small	intestine
46	chr4:143276000-143277000	Enhancers	Fetal Thymus	thymus
47	chr4:143276000-143277000	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr4:143276000-143277000	Enhancers	HSMMtube	muscle
49	chr4:143276200-143277600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr4:143276200-143277600	Weak transcription	HMEC	breast

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