Variant report

Variant	rs843764
Chromosome Location	chr2:54455057-54455058
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1099252	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1099254	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11895807	0.82[ASN][1000 genomes]
rs1215143	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1682108	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1682111	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17045690	0.83[ASN][1000 genomes]
rs1727504	0.92[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1727527	0.87[EUR][1000 genomes]
rs2695649	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs698751	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs698752	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs843648	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs843651	0.80[YRI][hapmap]
rs843662	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs843663	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs843666	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs843671	0.85[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap]
rs843672	0.94[CHB][hapmap];0.91[JPT][hapmap]
rs843711	0.83[YRI][hapmap]
rs843740	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs843754	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs843756	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs843760	0.85[EUR][1000 genomes]
rs843763	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs843765	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs843767	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs860057	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs863622	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1000652	chr2:54345892-54469703	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1009828	chr2:54393122-54488721	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv525086	chr2:54432222-54459211	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv532512	chr2:54453210-54630755	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54387800-54457400	Weak transcription	Aorta	Aorta
2	chr2:54442200-54456400	Weak transcription	Liver	Liver
3	chr2:54448600-54459400	Weak transcription	Esophagus	oesophagus
4	chr2:54448800-54459400	Weak transcription	HSMM	muscle
5	chr2:54449800-54535200	Weak transcription	Primary T cells from cord blood	blood
6	chr2:54450200-54455800	Weak transcription	Psoas Muscle	Psoas
7	chr2:54451600-54459400	Weak transcription	Left Ventricle	heart
8	chr2:54452400-54468000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:54452800-54490200	Weak transcription	Primary B cells from cord blood	blood
10	chr2:54453000-54456800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:54453600-54455800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:54453600-54459000	Weak transcription	HMEC	breast
13	chr2:54453800-54456000	Weak transcription	Fetal Kidney	kidney
14	chr2:54453800-54456200	Weak transcription	Osteobl	bone
15	chr2:54453800-54460400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:54453800-54466200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:54454000-54455200	Weak transcription	Adipose Nuclei	Adipose
18	chr2:54454000-54455800	Weak transcription	Ovary	ovary
19	chr2:54454000-54456000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:54454000-54456000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:54454000-54456000	Weak transcription	Brain Anterior Caudate	brain
22	chr2:54454200-54455800	Weak transcription	Brain Substantia Nigra	brain
23	chr2:54454200-54456200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:54454400-54455400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:54454600-54455600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:54454600-54455800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr2:54455000-54455200	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr2:54455000-54455200	Enhancers	K562	blood
29	chr2:54455000-54455400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:54455000-54455400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:54455000-54455800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:54455000-54455800	Enhancers	Fetal Heart	heart
33	chr2:54455000-54456400	Enhancers	Fetal Lung	lung
34	chr2:54455000-54457000	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links