Variant report

Variant	rs2838691
Chromosome Location	chr21:46223571-46223572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:46220877-46225649	K562	blood:	n/a	n/a
2	CTCF	chr21:46223500-46223650	SAEC	small airway:	n/a	n/a
3	POLR2A	chr21:46220980-46225308	K562	blood:	n/a	n/a
4	POLR2A	chr21:46221338-46225872	GM12878	blood:	n/a	n/a
5	POLR2A	chr21:46223465-46225324	HCT-116	colon:	n/a	n/a
6	POLR2A	chr21:46220710-46226000	K562	blood:	n/a	n/a
7	POLR2A	chr21:46220981-46225932	K562	blood:	n/a	n/a
8	POLR2A	chr21:46221323-46224680	GM12892	blood:	n/a	n/a
9	POLR2A	chr21:46221514-46223986	GM12878	blood:	n/a	n/a
10	USF2	chr21:46223537-46223893	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr21:46220458-46225731	K562	blood:	n/a	n/a
12	POLR2A	chr21:46223272-46225438	GM12892	blood:	n/a	n/a
13	CEBPB	chr21:46223376-46223953	K562	blood:	n/a	n/a
14	TAL1	chr21:46223441-46223998	K562	blood:	n/a	n/a
15	TEAD4	chr21:46223528-46224020	K562	blood:	n/a	n/a
16	POLR2A	chr21:46222035-46224585	GM12892	blood:	n/a	n/a
17	HCFC1	chr21:46223519-46223845	K562	blood:	n/a	n/a
18	MYC	chr21:46223477-46223886	K562	blood:	n/a	n/a
19	POLR2A	chr21:46221076-46225970	GM12878	blood:	n/a	n/a
20	POLR2A	chr21:46222351-46225533	GM12878	blood:	n/a	n/a
21	POLR2A	chr21:46221326-46226084	HepG2	liver:	n/a	n/a
22	CEBPB	chr21:46223554-46223934	K562	blood:	n/a	n/a
23	POLR2A	chr21:46221340-46225636	GM12892	blood:	n/a	n/a
24	POLR2A	chr21:46220647-46225708	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr21:46221298-46224011	MCF-7	breast:	n/a	n/a
26	POLR2A	chr21:46220865-46226037	GM12891	blood:	n/a	n/a
27	POLR2A	chr21:46221412-46224646	GM12891	blood:	n/a	n/a
28	POLR2A	chr21:46223376-46225822	Raji	blood:	n/a	n/a
29	POLR2A	chr21:46223315-46223633	GM12891	blood:	n/a	n/a
30	MAFK	chr21:46223376-46223958	K562	blood:	n/a	n/a
31	POLR2A	chr21:46223566-46225559	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr21:46222085-46225519	GM12891	blood:	n/a	n/a
33	CHD2	chr21:46223350-46223700	K562	blood:	n/a	n/a
34	POLR2A	chr21:46221550-46227421	K562	blood:	n/a	n/a
35	POLR2A	chr21:46222278-46224311	GM12891	blood:	n/a	n/a
36	PML	chr21:46222232-46224061	K562	blood:	n/a	n/a
37	POLR2A	chr21:46220826-46224367	PBDE	blood:	n/a	n/a
38	USF2	chr21:46223376-46224052	K562	blood:	n/a	n/a
39	POLR2A	chr21:46222376-46225739	HepG2	liver:	n/a	n/a
40	POLR2A	chr21:46221486-46225982	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr21:46221077-46225480	PFSK-1	brain:	n/a	n/a
42	POLR2A	chr21:46223316-46224648	K562	blood:	n/a	n/a
43	POLR2A	chr21:46223028-46223890	MCF10A-Er-Src	breast:	n/a	n/a
44	NRF1	chr21:46223220-46223658	K562	blood:	n/a	n/a
45	ZMIZ1	chr21:46223392-46223963	K562	blood:	n/a	n/a
46	POLR2A	chr21:46223276-46224272	K562	blood:	n/a	n/a
47	CTCF	chr21:46223547-46223944	K562	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46218606..46224662-chr21:46357422..46363606,13	MCF-7	breast:
2	chr21:46222712..46224808-chr21:46281066..46282729,2	MCF-7	breast:
3	chr21:46220974..46223841-chr21:46346856..46349461,2	K562	blood:
4	chr21:46220554..46223722-chr21:46306934..46310028,3	MCF-7	breast:
5	chr21:46220974..46223825-chr21:46494380..46498218,5	MCF-7	breast:
6	chr21:46223417..46225728-chr21:46304439..46306955,2	K562	blood:
7	chr1:110881656..110882311-chr21:46223033..46223646,2	NB4	blood:
8	chr21:46220930..46225769-chr21:46292170..46294469,5	K562	blood:
9	chr21:46220413..46223818-chr21:46291771..46295209,8	K562	blood:
10	chr21:45927714..45931885-chr21:46220128..46224260,6	MCF-7	breast:
11	chr21:46217105..46224485-chr21:46287607..46297526,26	MCF-7	breast:
12	chr21:46220228..46226309-chr21:46349546..46355767,8	K562	blood:

No data

Variant related genes	Relation type
UBE2G2	TF binding region
ENSG00000235890	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000273027	Chromatin interaction
ENSG00000162775	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000227963	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000183250	Chromatin interaction
ENSG00000160255	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1051331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1141	1.00[CEU][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17217834	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17289578	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17289745	1.00[CEU][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2017089	1.00[CEU][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2838689	1.00[CEU][hapmap];0.82[LWK][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2838690	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838692	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28728356	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8645	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs873301	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9975507	1.00[CHB][hapmap]
rs9977480	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9977684	1.00[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9984357	0.97[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
rs2838691	PCBP3	cis	parietal	SCAN
rs2838691	UBE2G2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46222400-46236400	Weak transcription	Small Intestine	intestine
2	chr21:46222600-46223600	Transcr. at gene 5' and 3'	K562	blood
3	chr21:46222600-46224600	Weak transcription	Brain Angular Gyrus	brain
4	chr21:46222600-46224800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr21:46222600-46224800	Weak transcription	Aorta	Aorta
6	chr21:46222600-46224800	Weak transcription	Left Ventricle	heart
7	chr21:46222600-46224800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr21:46222600-46225000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr21:46222600-46226200	Weak transcription	Esophagus	oesophagus
10	chr21:46222600-46226800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr21:46222600-46234800	Weak transcription	Right Atrium	heart
12	chr21:46222600-46236400	Weak transcription	Stomach Mucosa	stomach
13	chr21:46222600-46237200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr21:46222800-46223600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr21:46222800-46224000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr21:46222800-46224200	Weak transcription	Primary T cells from cord blood	blood
17	chr21:46222800-46224200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr21:46222800-46224600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr21:46222800-46224800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr21:46222800-46224800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr21:46222800-46224800	Weak transcription	Brain Substantia Nigra	brain
22	chr21:46222800-46224800	Weak transcription	Fetal Brain Female	brain
23	chr21:46222800-46224800	Weak transcription	Ovary	ovary
24	chr21:46222800-46224800	Weak transcription	Pancreas	Pancrea
25	chr21:46222800-46224800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr21:46222800-46224800	Weak transcription	Thymus	Thymus
27	chr21:46222800-46224800	Weak transcription	NHDF-Ad	bronchial
28	chr21:46222800-46225000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr21:46222800-46225000	Weak transcription	Brain Hippocampus Middle	brain
30	chr21:46222800-46225200	Weak transcription	Fetal Brain Male	brain
31	chr21:46222800-46225200	Weak transcription	Fetal Kidney	kidney
32	chr21:46222800-46225400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr21:46222800-46226400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr21:46222800-46226400	Weak transcription	Gastric	stomach
35	chr21:46222800-46226600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr21:46222800-46236400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr21:46222800-46237200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr21:46223000-46223600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr21:46223000-46223600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr21:46223000-46223600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr21:46223000-46223600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr21:46223000-46223600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr21:46223000-46223600	Genic enhancers	Dnd41	blood
44	chr21:46223000-46223800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr21:46223000-46223800	Weak transcription	Colon Smooth Muscle	Colon
46	chr21:46223000-46223800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr21:46223000-46224000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr21:46223000-46224000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
49	chr21:46223000-46224400	Weak transcription	Primary B cells from cord blood	blood
50	chr21:46223000-46224400	Weak transcription	Primary T cells fromperipheralblood	blood

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