Variant report

Variant	rs11680892
Chromosome Location	chr2:31436308-31436309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11124248	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11124249	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11124250	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11124251	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11124255	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11681503	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11681673	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11687767	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11692905	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12619774	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12619859	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12623398	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1373218	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1373219	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17011001	0.88[JPT][hapmap]
rs4952068	0.86[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4952069	0.88[JPT][hapmap]
rs6543617	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7585737	0.88[JPT][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs7591444	0.89[JPT][hapmap]
rs9789485	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[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	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv873775	chr2:31363732-31439443	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv873776	chr2:31384009-31439443	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv430635	chr2:31420415-31464385	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1009712	chr2:31424588-31468364	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription 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	3 gene(s)	inside rSNPs	diseases
6	nsv1000416	chr2:31424588-31470845	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv581268	chr2:31425783-31467079	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1001299	chr2:31428030-31464385	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv430646	chr2:31428030-31464385	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv1010164	chr2:31436026-31439821	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11680892	EHD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31411200-31436800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:31423400-31436800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:31424200-31437600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:31428800-31437400	Weak transcription	Esophagus	oesophagus
5	chr2:31430200-31441600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:31431800-31436800	Weak transcription	Primary B cells from cord blood	blood
7	chr2:31432400-31436600	Weak transcription	Fetal Heart	heart
8	chr2:31435800-31437000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:31435800-31437200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr2:31435800-31439800	Enhancers	GM12878-XiMat	blood
11	chr2:31436000-31436400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:31436000-31436400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr2:31436000-31436400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr2:31436000-31436400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr2:31436000-31436400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr2:31436000-31436400	Enhancers	Fetal Thymus	thymus
17	chr2:31436000-31436600	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr2:31436200-31437200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:31436200-31440200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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