Variant report

Variant	rs4239838
Chromosome Location	chr21:46202309-46202310
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46202272..46204330-chr21:46240316..46243061,2	K562	blood:
2	chr21:46198042..46200426-chr21:46201214..46204112,4	K562	blood:
3	chr21:46182055..46185052-chr21:46201680..46204266,2	MCF-7	breast:
4	chr21:46192937..46195501-chr21:46201890..46203698,2	MCF-7	breast:
5	chr21:46177180..46179450-chr21:46200338..46203449,3	MCF-7	breast:
6	chr21:46197791..46202676-chr21:46204066..46207240,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184787	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1071792	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11088963	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1109280	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11701732	0.93[ASN][1000 genomes]
rs11702064	0.89[CHB][hapmap];0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs11702743	0.88[ASN][1000 genomes]
rs13049657	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs13050872	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1347324	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1821431	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294157	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329899	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2329900	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2838673	0.84[EUR][1000 genomes]
rs2838675	0.84[CEU][hapmap];0.85[CHD][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs2838678	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838699	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs35209090	1.00[ASN][1000 genomes]
rs35242981	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35933313	1.00[ASN][1000 genomes]
rs3788136	1.00[CEU][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4818734	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4818973	0.84[EUR][1000 genomes]
rs4818974	0.84[EUR][1000 genomes]
rs4818975	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62220109	0.97[ASN][1000 genomes]
rs62222752	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6518204	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7281735	0.92[ASN][1000 genomes]
rs733161	0.84[EUR][1000 genomes]
rs760430	0.85[CHD][hapmap]
rs760431	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap]
rs760432	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8103	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128992	0.80[EUR][1000 genomes]
rs8133039	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs885655	0.84[CEU][hapmap];0.85[CHD][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs885656	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs885657	0.84[CEU][hapmap];0.85[CHD][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4239838	UBE2G2	Cis_1M	lymphoblastoid	RTeQTL
rs4239838	C21orf58	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46187000-46213000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr21:46187800-46206200	Strong transcription	Fetal Thymus	thymus
3	chr21:46188000-46203000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr21:46188000-46203200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr21:46188000-46208000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr21:46188600-46208000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr21:46189000-46221000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr21:46189200-46203000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr21:46189600-46203600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr21:46189600-46207800	Strong transcription	Dnd41	blood
11	chr21:46190800-46209600	Weak transcription	Fetal Brain Male	brain
12	chr21:46193400-46212600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr21:46193800-46206000	Weak transcription	Brain Hippocampus Middle	brain
14	chr21:46193800-46212800	Weak transcription	Psoas Muscle	Psoas
15	chr21:46194800-46203200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr21:46195000-46211200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr21:46195000-46212600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr21:46195000-46219800	Weak transcription	Small Intestine	intestine
19	chr21:46195200-46204600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr21:46195400-46220400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr21:46195600-46211400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr21:46195800-46203200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr21:46196000-46205600	Weak transcription	Brain Anterior Caudate	brain
24	chr21:46196000-46211800	Weak transcription	NHLF	lung
25	chr21:46196800-46203400	Weak transcription	Brain Germinal Matrix	brain
26	chr21:46197000-46203200	Weak transcription	Fetal Brain Female	brain
27	chr21:46197200-46213000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr21:46197200-46220400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr21:46197400-46203000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr21:46197400-46204800	Weak transcription	Brain Substantia Nigra	brain
31	chr21:46197400-46212800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr21:46198000-46207200	Weak transcription	NH-A	brain
33	chr21:46198200-46204800	Weak transcription	Placenta	Placenta
34	chr21:46198400-46207200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr21:46198600-46203200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr21:46198600-46204600	Weak transcription	Fetal Intestine Large	intestine
37	chr21:46198600-46212000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr21:46198800-46202800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr21:46198800-46204200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr21:46198800-46208000	Strong transcription	K562	blood
41	chr21:46198800-46211400	Weak transcription	HUVEC	blood vessel
42	chr21:46198800-46213000	Weak transcription	Brain Angular Gyrus	brain
43	chr21:46198800-46219600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr21:46198800-46220000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr21:46198800-46220000	Weak transcription	Fetal Kidney	kidney
46	chr21:46199200-46202600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr21:46199200-46207000	Weak transcription	Osteobl	bone
48	chr21:46199600-46203600	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr21:46199800-46202400	Strong transcription	GM12878-XiMat	blood
50	chr21:46199800-46204600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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