Variant report

Variant	rs843729
Chromosome Location	chr2:54516182-54516183
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1682102	0.90[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1682121	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs698756	0.86[JPT][hapmap]
rs843716	0.94[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs843717	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs843718	0.95[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs843719	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs843720	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs843721	0.93[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs843722	0.93[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs843723	0.91[ASN][1000 genomes]
rs843724	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs843725	0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs843727	0.82[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs843728	0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs843730	0.90[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs843731	0.90[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs843732	0.93[CHB][hapmap];0.89[ASN][1000 genomes]
rs843733	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs843734	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs843768	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs843769	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs860056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
8	nsv1004632	chr2:54469283-54590480	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv998172	chr2:54488511-54537474	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1011754	chr2:54494644-54533805	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv14065	chr2:54513051-54517656	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
12	esv3459572	chr2:54513069-54517863	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
13	esv3459573	chr2:54513117-54517838	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
14	esv3459575	chr2:54513215-54517733	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
15	nsv961317	chr2:54516070-54516570	Bivalent Enhancer Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54449800-54535200	Weak transcription	Primary T cells from cord blood	blood
2	chr2:54483400-54521200	Weak transcription	Pancreas	Pancrea
3	chr2:54500200-54517800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr2:54501600-54537600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:54513000-54516400	Weak transcription	Primary B cells from cord blood	blood
6	chr2:54514800-54516800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
7	chr2:54514800-54517200	Weak transcription	Aorta	Aorta
8	chr2:54515000-54516800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
9	chr2:54515000-54516800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
10	chr2:54515200-54516800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
11	chr2:54515200-54517000	Weak transcription	Brain Angular Gyrus	brain
12	chr2:54515200-54517000	Weak transcription	Brain Anterior Caudate	brain
13	chr2:54515200-54517000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:54515200-54517200	Weak transcription	Left Ventricle	heart
15	chr2:54515200-54518200	Weak transcription	Right Atrium	heart
16	chr2:54515200-54522600	Weak transcription	Psoas Muscle	Psoas
17	chr2:54515200-54526200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:54515400-54517000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:54515400-54518000	Weak transcription	HSMMtube	muscle
20	chr2:54515600-54516200	Enhancers	Fetal Intestine Small	intestine
21	chr2:54515800-54516200	Enhancers	HepG2	liver
22	chr2:54515800-54516800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
23	chr2:54515800-54516800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
24	chr2:54515800-54517000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:54516000-54517200	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:54516000-54520200	Weak transcription	Fetal Kidney	kidney

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