Variant report

Variant	rs2838689
Chromosome Location	chr21:46220610-46220611
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr21:46220460-46220610	GM06990	blood:	n/a	n/a
2	GATA3	chr21:46220415-46221082	SH-SY5Y	brain:	n/a	n/a
3	CTCF	chr21:46219714-46220665	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr21:46220458-46225731	K562	blood:	n/a	n/a
5	MXI1	chr21:46219626-46223381	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr21:46220561-46221500	A549	lung:	n/a	n/a
7	IRF1	chr21:46220109-46222291	K562	blood:	n/a	n/a
8	CTCF	chr21:46220460-46220610	AG10803	skin:	n/a	n/a
9	RAD21	chr21:46219791-46222163	SK-N-SH	brain:	n/a	n/a
10	CTCF	chr21:46219999-46221390	K562	blood:	n/a	n/a
11	HCFC1	chr21:46220297-46223080	Hela-S3	cervix:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46218606..46224662-chr21:46357422..46363606,13	MCF-7	breast:
2	chr21:46220374..46222087-chr21:46311415..46314337,2	MCF-7	breast:
3	chr21:45928985..45931297-chr21:46219796..46221889,2	MCF-7	breast:
4	chr21:46218558..46223428-chr21:46289542..46296056,15	MCF-7	breast:
5	chr21:45718752..45721154-chr21:46219831..46222611,2	K562	blood:
6	chr21:46220554..46223722-chr21:46306934..46310028,3	MCF-7	breast:
7	chr21:46219434..46222664-chr21:46346417..46349763,6	MCF-7	breast:
8	chr21:46220151..46222677-chr21:46492186..46495962,3	K562	blood:
9	chr21:46219802..46220657-chr21:46291980..46292897,2	MCF-7	breast:
10	chr21:46220083..46220610-chr21:46295309..46295835,2	MCF-7	breast:
11	chr21:46218496..46222154-chr21:46279503..46283710,3	MCF-7	breast:
12	chr21:46220413..46223818-chr21:46291771..46295209,8	K562	blood:
13	chr21:46219770..46220689-chr21:46548247..46548881,2	MCF-7	breast:
14	chr21:46220308..46222402-chr21:46328701..46333083,4	MCF-7	breast:
15	chr21:45927714..45931885-chr21:46220128..46224260,6	MCF-7	breast:
16	chr21:46220260..46222802-chr21:46358731..46365262,8	MCF-7	breast:
17	chr20:45984634..45987262-chr21:46219843..46222143,2	MCF-7	breast:
18	chr21:46220183..46220714-chr21:46556779..46557402,2	MCF-7	breast:
19	chr21:46217105..46224485-chr21:46287607..46297526,26	MCF-7	breast:
20	chr21:46220263..46223201-chr21:46349640..46352735,4	K562	blood:
21	chr21:46219746..46220652-chr21:46256461..46257271,3	MCF-7	breast:
22	chr21:46220228..46226309-chr21:46349546..46355767,8	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTTG1IP-1	chr21:46219905-46221313	NONHSAT082879

No data

Variant related genes	Relation type
ENSG00000236519	TF binding region
ENSG00000160255	Chromatin interaction
ENSG00000273027	Chromatin interaction
ENSG00000183250	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000268856	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000141959	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000235890	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1051331	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs1141	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17217834	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17289578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17289745	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017089	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838681	1.00[ASN][1000 genomes]
rs2838683	1.00[ASN][1000 genomes]
rs2838690	1.00[CEU][hapmap];0.82[LWK][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2838691	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]
rs2838692	1.00[CEU][hapmap]
rs28728356	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs428428	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232950	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8645	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs873301	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9977684	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2838689	PCBP3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46189000-46221000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:46205200-46220800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr21:46218800-46220800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr21:46219200-46220800	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr21:46219200-46220800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr21:46219400-46220800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr21:46219400-46221000	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr21:46219600-46220800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr21:46219600-46221400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr21:46219800-46220800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr21:46219800-46220800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr21:46219800-46220800	Enhancers	Brain Substantia Nigra	brain
13	chr21:46219800-46220800	Enhancers	Ovary	ovary
14	chr21:46219800-46220800	Enhancers	Pancreas	Pancrea
15	chr21:46219800-46220800	Enhancers	Stomach Mucosa	stomach
16	chr21:46219800-46221000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr21:46219800-46221000	Enhancers	Primary B cells from peripheral blood	blood
18	chr21:46219800-46221000	Flanking Active TSS	GM12878-XiMat	blood
19	chr21:46219800-46221000	Transcr. at gene 5' and 3'	K562	blood
20	chr21:46219800-46222400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr21:46220000-46220800	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr21:46220000-46220800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr21:46220000-46220800	Enhancers	Esophagus	oesophagus
24	chr21:46220000-46220800	Enhancers	Placenta	Placenta
25	chr21:46220000-46220800	Enhancers	Left Ventricle	heart
26	chr21:46220000-46220800	Enhancers	Lung	lung
27	chr21:46220000-46221000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr21:46220000-46221000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr21:46220000-46221000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr21:46220000-46221000	Flanking Active TSS	Fetal Brain Male	brain
31	chr21:46220000-46221000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr21:46220000-46221000	Flanking Active TSS	HMEC	breast
33	chr21:46220000-46221200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr21:46220000-46221200	Flanking Active TSS	Osteobl	bone
35	chr21:46220000-46221600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr21:46220000-46222400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr21:46220200-46220800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr21:46220200-46220800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr21:46220200-46220800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr21:46220200-46220800	Enhancers	Primary T cells fromperipheralblood	blood
41	chr21:46220200-46220800	Enhancers	Small Intestine	intestine
42	chr21:46220200-46221000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr21:46220200-46221000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr21:46220200-46221000	Flanking Active TSS	Hela-S3	cervix
45	chr21:46220200-46221200	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr21:46220200-46221200	Flanking Active TSS	Fetal Brain Female	brain
47	chr21:46220200-46221200	Flanking Active TSS	HUVEC	blood vessel
48	chr21:46220200-46221600	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr21:46220200-46222600	Active TSS	Fetal Kidney	kidney
50	chr21:46220200-46222600	Active TSS	A549	lung

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