Variant report

Variant	rs698756
Chromosome Location	chr2:54523285-54523286
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: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1682102	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs843716	0.83[CHB][hapmap]
rs843718	0.89[CHB][hapmap]
rs843719	0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs843720	0.84[CHB][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs843721	0.80[ASW][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs843722	0.84[CHB][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs843723	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs843724	0.82[JPT][hapmap]
rs843725	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs843727	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs843728	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs843729	0.86[JPT][hapmap]
rs843730	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs843731	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs843732	0.83[CHB][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs843768	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs860056	0.82[CEU][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]

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
rs698756	C2orf73	cis	brain	BrainEAC

Chromatin state (count:20 , 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	chr2:54501600-54537600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:54515200-54526200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:54517600-54536800	Weak transcription	Aorta	Aorta
5	chr2:54517800-54537200	Weak transcription	Brain Anterior Caudate	brain
6	chr2:54518400-54525600	Weak transcription	HSMMtube	muscle
7	chr2:54518600-54530000	Weak transcription	Right Atrium	heart
8	chr2:54522600-54523400	Enhancers	Psoas Muscle	Psoas
9	chr2:54523000-54523400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr2:54523000-54523400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:54523000-54523400	Enhancers	Lung	lung
12	chr2:54523200-54523400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:54523200-54523400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr2:54523200-54523400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr2:54523200-54523600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr2:54523200-54523600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:54523200-54523600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr2:54523200-54523600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr2:54523200-54523600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:54523200-54523600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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