Variant report

Variant	rs843731
Chromosome Location	chr2:54517956-54517957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54516670..54519099-chr2:54522119..54523673,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1682102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1682121	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs698752	0.83[CHB][hapmap]
rs698756	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs843672	0.83[CHB][hapmap]
rs843716	0.89[CHB][hapmap];0.83[AMR][1000 genomes]
rs843717	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs843718	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs843719	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs843720	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs843721	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs843722	1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs843723	0.97[ASN][1000 genomes]
rs843724	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs843725	0.82[JPT][hapmap]
rs843727	0.82[JPT][hapmap]
rs843728	0.82[JPT][hapmap]
rs843729	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]
rs843730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs843732	0.94[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.87[ASN][1000 genomes]
rs843733	0.91[CEU][hapmap];0.94[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs843734	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs843754	0.83[CHB][hapmap]
rs843768	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs843769	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs860056	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs863622	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv997896	chr2:54517853-54549501	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs843731	RPL23AP32	cis	cerebellum	SCAN

Chromatin state (count:25 , 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	chr2:54501600-54537600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:54515200-54518200	Weak transcription	Right Atrium	heart
5	chr2:54515200-54522600	Weak transcription	Psoas Muscle	Psoas
6	chr2:54515200-54526200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:54515400-54518000	Weak transcription	HSMMtube	muscle
8	chr2:54516000-54520200	Weak transcription	Fetal Kidney	kidney
9	chr2:54517000-54518000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
10	chr2:54517000-54518000	Enhancers	Fetal Brain Male	brain
11	chr2:54517200-54518600	Enhancers	Fetal Stomach	stomach
12	chr2:54517600-54518000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
13	chr2:54517600-54518200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
14	chr2:54517600-54518200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:54517600-54518400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:54517600-54519000	Enhancers	Fetal Muscle Leg	muscle
17	chr2:54517600-54521800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:54517600-54536800	Weak transcription	Aorta	Aorta
19	chr2:54517800-54518000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
20	chr2:54517800-54518000	Enhancers	Primary B cells from peripheral blood	blood
21	chr2:54517800-54518200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
22	chr2:54517800-54518200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
23	chr2:54517800-54518200	Enhancers	Brain Angular Gyrus	brain
24	chr2:54517800-54518400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
25	chr2:54517800-54537200	Weak transcription	Brain Anterior Caudate	brain

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