Variant report

Variant	rs6660043
Chromosome Location	chr1:227496438-227496439
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:21)

rs_ID	r²[population]
rs10799411	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10916117	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12033050	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12035190	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];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12035998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs12038272	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[ASN][1000 genomes]
rs12073573	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12079122	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12079173	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12080452	0.83[EUR][1000 genomes]
rs12095674	0.83[EUR][1000 genomes]
rs4065211	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4653828	0.86[ASW][hapmap]
rs61700597	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61834325	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834563	0.83[EUR][1000 genomes]
rs61834564	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6699534	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72757311	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7513122	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227462600-227500200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:227469200-227500200	Weak transcription	Left Ventricle	heart
3	chr1:227469200-227502600	Weak transcription	HSMM	muscle
4	chr1:227469600-227501800	Weak transcription	Fetal Stomach	stomach
5	chr1:227475000-227502000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:227475200-227500200	Weak transcription	Fetal Intestine Small	intestine
7	chr1:227483600-227500200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:227483800-227500400	Weak transcription	Right Atrium	heart
9	chr1:227486600-227497800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:227487000-227500200	Weak transcription	HMEC	breast
11	chr1:227487000-227501800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:227487000-227501800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:227487000-227502000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:227487600-227496800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:227487600-227497600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:227487600-227502400	Weak transcription	Osteobl	bone
17	chr1:227487800-227497000	Weak transcription	Fetal Lung	lung
18	chr1:227487800-227497200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:227487800-227500200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:227487800-227500400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:227487800-227501400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:227488000-227501800	Weak transcription	A549	lung
23	chr1:227490200-227503800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:227491400-227501400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:227491600-227499200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:227491800-227497800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:227492000-227497200	Weak transcription	Brain Angular Gyrus	brain
28	chr1:227492200-227498000	Weak transcription	Psoas Muscle	Psoas
29	chr1:227492600-227503400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr1:227493200-227499400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:227494200-227498000	Weak transcription	Small Intestine	intestine
32	chr1:227494200-227500200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:227494400-227500200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:227494600-227496600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:227494600-227497400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:227494800-227497800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:227495000-227496600	Weak transcription	Brain Anterior Caudate	brain
38	chr1:227495000-227500200	Weak transcription	Brain Substantia Nigra	brain
39	chr1:227495000-227503400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:227495800-227497000	Enhancers	Stomach Mucosa	stomach
41	chr1:227495800-227498200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:227496000-227497200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:227496000-227498400	Enhancers	Adipose Nuclei	Adipose
44	chr1:227496200-227496600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:227496200-227498000	Enhancers	Brain Hippocampus Middle	brain
46	chr1:227496200-227498400	Enhancers	Fetal Heart	heart
47	chr1:227496200-227500200	Weak transcription	Pancreas	Pancrea
48	chr1:227496200-227502000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:227496200-227504800	Weak transcription	Gastric	stomach
50	chr1:227496400-227496600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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