Variant report

Variant	rs2838293
Chromosome Location	chr21:44806314-44806315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:44784945..44787524-chr21:44806309..44807951,2	MCF-7	breast:
2	chr21:44804088..44806777-chr21:44809162..44811589,2	K562	blood:
3	chr21:44780389..44782566-chr21:44805407..44807925,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237989	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1003791	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1003792	0.88[ASN][1000 genomes]
rs11910909	0.82[CHB][hapmap]
rs12627203	0.86[CHB][hapmap]
rs2073429	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838292	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2838295	0.94[CEU][hapmap];0.95[CHB][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2838296	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4818721	0.88[ASN][1000 genomes]
rs4818928	0.90[ASN][1000 genomes]
rs55837771	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66932133	0.88[ASN][1000 genomes]
rs67059973	0.83[ASN][1000 genomes]
rs67784679	0.85[ASN][1000 genomes]
rs9979820	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056684	chr21:44539714-44886119	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv913831	chr21:44563995-44931821	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
3	esv1817359	chr21:44699077-44821595	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057726	chr21:44711850-44957303	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised 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 miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv544466	chr21:44711850-44957303	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
6	nsv1058308	chr21:44722915-44825108	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1063186	chr21:44729904-44828476	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv544467	chr21:44729904-44828476	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv913837	chr21:44731138-44853859	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv913838	chr21:44740134-44931821	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
11	nsv913839	chr21:44750200-44931821	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
12	nsv913840	chr21:44750643-44823479	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
13	nsv913841	chr21:44761874-44853859	Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
14	nsv913843	chr21:44774757-44810756	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv913844	chr21:44779680-44875495	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
16	nsv913845	chr21:44781356-44874702	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
17	nsv470901	chr21:44781356-44884252	Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
18	nsv913846	chr21:44792003-44824854	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
19	nsv913847	chr21:44792003-44931821	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
20	esv3427724	chr21:44803524-44806822	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2838293	LOC284837	cis	parietal	SCAN
rs2838293	NCRNA00257	cis	parietal	SCAN
rs2838293	DSCAM	cis	parietal	SCAN
rs2838293	MARCKS	trans	lymphoblastoid	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44790600-44830800	Weak transcription	Right Atrium	heart
2	chr21:44795400-44814200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr21:44800200-44808400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr21:44800400-44814200	Weak transcription	Hela-S3	cervix
5	chr21:44802600-44806600	Enhancers	Fetal Thymus	thymus
6	chr21:44802600-44810000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr21:44803000-44809200	Enhancers	Fetal Brain Male	brain
8	chr21:44803400-44808000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr21:44803600-44807400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr21:44803800-44807000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr21:44803800-44807000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr21:44803800-44807000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr21:44803800-44807200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr21:44803800-44807200	Weak transcription	Fetal Lung	lung
15	chr21:44803800-44807400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr21:44803800-44807400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr21:44803800-44807400	Weak transcription	Brain Anterior Caudate	brain
18	chr21:44803800-44807400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr21:44804000-44806600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr21:44804000-44807000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr21:44804000-44807000	Weak transcription	Brain Hippocampus Middle	brain
22	chr21:44804000-44807000	Weak transcription	Fetal Muscle Leg	muscle
23	chr21:44804000-44807400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr21:44804000-44807400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr21:44804400-44807200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr21:44804400-44819000	Weak transcription	Gastric	stomach
27	chr21:44804600-44806600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr21:44804600-44807000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr21:44804600-44807400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr21:44804600-44808200	Enhancers	HMEC	breast
31	chr21:44805000-44806800	Weak transcription	Esophagus	oesophagus
32	chr21:44805000-44807400	Enhancers	Fetal Brain Female	brain
33	chr21:44805200-44807400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr21:44805600-44806400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr21:44805800-44806800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr21:44806000-44807400	Enhancers	Brain Germinal Matrix	brain
37	chr21:44806200-44806600	Weak transcription	Spleen	Spleen
38	chr21:44806200-44808400	Enhancers	Cortex derived primary cultured neurospheres	brain

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