Variant report

Variant	rs1346943
Chromosome Location	chr3:150824794-150824795
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	chr3:150814792..150816660-chr3:150824326..150826641,2	MCF-7	breast:
2	chr3:150824339..150827241-chr3:150830222..150833263,3	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10755104	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10935825	0.82[GIH][hapmap]
rs10935827	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10935828	0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11914598	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12489984	0.90[ASN][1000 genomes]
rs12634353	1.00[ASW][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];0.93[AFR][1000 genomes]
rs13434276	0.87[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16863172	1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1835668	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1897296	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2014240	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2043171	0.82[EUR][1000 genomes]
rs58990954	0.89[EUR][1000 genomes]
rs6414377	0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6765711	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs6767918	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6772640	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6787683	0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6790661	0.90[ASN][1000 genomes]
rs747205	0.90[ASN][1000 genomes]
rs965843	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9683109	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs970235	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9813224	0.90[ASN][1000 genomes]
rs9822304	0.95[ASN][1000 genomes]
rs9829728	0.83[ASN][1000 genomes]
rs9848163	0.89[ASN][1000 genomes]
rs9850016	0.96[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9883677	1.00[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915879	chr3:150607390-150860207	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv829756	chr3:150692636-150889738	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv877648	chr3:150792444-150895145	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1346943	DHX36	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150809800-150827400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:150812000-150824800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:150819800-150825000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:150819800-150825000	Weak transcription	Brain Anterior Caudate	brain
5	chr3:150819800-150825600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:150819800-150827600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:150819800-150847600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:150820000-150825000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:150820200-150825200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:150820600-150825600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:150820800-150825000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:150820800-150825200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:150820800-150840000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:150822400-150825000	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:150823200-150843000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr3:150823400-150826800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:150823600-150826000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:150824000-150825000	Weak transcription	Placenta	Placenta
19	chr3:150824000-150825800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:150824200-150825000	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr3:150824400-150826000	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:150824400-150826600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:150824400-150826600	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr3:150824400-150826600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr3:150824400-150826800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:150824600-150826200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:150824600-150826600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr3:150824600-150826800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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