Variant report

Variant	rs2838690
Chromosome Location	chr21:46222486-46222487
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr21:46222380-46222530	GM12868	blood:	n/a	n/a
2	MAX	chr21:46220947-46222556	Hela-S3	cervix:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
3	CTCF	chr21:46222460-46222610	HCPEpiC	choroid plexus:	n/a	n/a
4	CTCF	chr21:46222380-46222530	Hela-S3	cervix:	n/a	n/a
5	MAZ	chr21:46221542-46223054	K562	blood:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
6	POLR2A	chr21:46220923-46223514	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr21:46221343-46222618	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr21:46221416-46222547	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr21:46221484-46222573	HCT-116	colon:	n/a	n/a
10	GABPA	chr21:46220816-46222492	MCF-7	breast:	n/a	chr21:46221780-46221791 chr21:46221782-46221791 chr21:46221780-46221794
11	MBD4	chr21:46222354-46223217	HepG2	liver:	n/a	n/a
12	ZBTB7A	chr21:46221892-46222612	K562	blood:	n/a	chr21:46222482-46222489
13	POLR2A	chr21:46221444-46222951	GM18951	blood:	n/a	n/a
14	POLR2A	chr21:46222424-46222734	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr21:46221357-46223210	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr21:46220971-46222659	K562	blood:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
17	POLR2A	chr21:46220877-46225649	K562	blood:	n/a	n/a
18	CTCF	chr21:46222380-46222530	GM12866	blood:	n/a	n/a
19	CTCF	chr21:46222360-46222510	K562	blood:	n/a	n/a
20	SIN3A	chr21:46220887-46222973	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr21:46221404-46222699	Hela-S3	cervix:	n/a	n/a
22	EGR1	chr21:46222361-46222666	K562	blood:	n/a	n/a
23	CTCF	chr21:46222380-46222530	GM12872	blood:	n/a	n/a
24	POLR2A	chr21:46220980-46225308	K562	blood:	n/a	n/a
25	POLR2A	chr21:46221338-46225872	GM12878	blood:	n/a	n/a
26	GTF2F1	chr21:46221629-46223000	Hela-S3	cervix:	n/a	n/a
27	TBP	chr21:46220886-46222735	K562	blood:	n/a	n/a
28	YY1	chr21:46222109-46222614	K562	blood:	n/a	chr21:46222430-46222441
29	MAX	chr21:46221015-46223263	HepG2	liver:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
30	POLR2A	chr21:46221413-46223236	ECC-1	luminal epithelium:	n/a	n/a
31	CTCF	chr21:46222400-46222550	GM12867	blood:	n/a	n/a
32	CCNT2	chr21:46221412-46222553	K562	blood:	n/a	chr21:46221544-46221553 chr21:46222087-46222096
33	MYC	chr21:46221506-46222919	K562	blood:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
34	POLR2A	chr21:46220710-46226000	K562	blood:	n/a	n/a
35	MAX	chr21:46220910-46222976	MCF-7	breast:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
36	POLR2A	chr21:46220981-46225932	K562	blood:	n/a	n/a
37	MAX	chr21:46222471-46222555	GM12878	blood:	n/a	n/a
38	ZNF143	chr21:46222411-46222560	GM12878	blood:	n/a	chr21:46222434-46222444
39	CTCF	chr21:46222400-46222550	GM12869	blood:	n/a	n/a
40	POLR2A	chr21:46221318-46222536	MCF-7	breast:	n/a	n/a
41	MAX	chr21:46221032-46222559	A549	lung:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
42	EGR1	chr21:46222343-46222724	K562	blood:	n/a	n/a
43	CTCF	chr21:46222360-46222510	GM12874	blood:	n/a	n/a
44	MYC	chr21:46220905-46223032	K562	blood:	n/a	chr21:46222000-46222009 chr21:46222236-46222243
45	ZNF384	chr21:46222265-46222509	K562	blood:	n/a	n/a
46	POLR2A	chr21:46221323-46224680	GM12892	blood:	n/a	n/a
47	HEY1	chr21:46222111-46222573	K562	blood:	n/a	n/a
48	POLR2A	chr21:46222410-46222760	GM12891	blood:	n/a	n/a
49	POLR2A	chr21:46221514-46223986	GM12878	blood:	n/a	n/a
50	CTCF	chr21:46222420-46222570	HMEC	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:46218606..46224662-chr21:46357422..46363606,13	MCF-7	breast:
2	chr21:46218558..46223428-chr21:46289542..46296056,15	MCF-7	breast:
3	chr21:45718752..45721154-chr21:46219831..46222611,2	K562	blood:
4	chr21:46220974..46223841-chr21:46346856..46349461,2	K562	blood:
5	chr21:46220554..46223722-chr21:46306934..46310028,3	MCF-7	breast:
6	chr21:46220974..46223825-chr21:46494380..46498218,5	MCF-7	breast:
7	chr21:46220726..46223224-chr21:46328113..46331561,4	K562	blood:
8	chr21:46219434..46222664-chr21:46346417..46349763,6	MCF-7	breast:
9	chr21:46220151..46222677-chr21:46492186..46495962,3	K562	blood:
10	chr21:46220930..46225769-chr21:46292170..46294469,5	K562	blood:
11	chr21:46221113..46222920-chr21:46311601..46314491,2	K562	blood:
12	chr21:46220413..46223818-chr21:46291771..46295209,8	K562	blood:
13	chr21:45927714..45931885-chr21:46220128..46224260,6	MCF-7	breast:
14	chr21:46220260..46222802-chr21:46358731..46365262,8	MCF-7	breast:
15	chr21:46217105..46224485-chr21:46287607..46297526,26	MCF-7	breast:
16	chr21:46220263..46223201-chr21:46349640..46352735,4	K562	blood:
17	chr21:46220228..46226309-chr21:46349546..46355767,8	K562	blood:

Variant related genes	Relation type
ENSG00000236519	TF binding region
UBE2G2	TF binding region
ENSG00000235890	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000183250	Chromatin interaction
ENSG00000160255	Chromatin interaction
ENSG00000273027	Chromatin interaction
ENSG00000268856	Chromatin interaction
ENSG00000141959	Chromatin interaction
ENSG00000160256	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];0.85[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];0.91[MKK][hapmap];0.90[TSI][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];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2838691	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];0.86[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
rs2838690	UBE2G2	cis	parietal	SCAN
rs2838690	PCBP3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46220200-46222600	Active TSS	Fetal Kidney	kidney
2	chr21:46220200-46222600	Active TSS	A549	lung
3	chr21:46220400-46222600	Active TSS	H1 Cell Line	embryonic stem cell
4	chr21:46220400-46222800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:46220400-46223000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr21:46220600-46222600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr21:46220600-46222600	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr21:46220600-46222800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr21:46220600-46222800	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr21:46220600-46222800	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr21:46220800-46222600	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr21:46220800-46222600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr21:46220800-46222600	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr21:46220800-46222600	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr21:46220800-46222600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr21:46220800-46222600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr21:46220800-46222600	Active TSS	NHLF	lung
18	chr21:46220800-46222800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr21:46220800-46222800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr21:46220800-46222800	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr21:46220800-46222800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
22	chr21:46220800-46223000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr21:46220800-46223000	Active TSS	HSMM	muscle
24	chr21:46221000-46222600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr21:46221000-46222600	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr21:46221000-46222600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr21:46221000-46222600	Active TSS	Muscle Satellite Cultured Cells	--
28	chr21:46221000-46222600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr21:46221000-46222600	Active TSS	Esophagus	oesophagus
30	chr21:46221000-46222600	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr21:46221000-46222600	Active TSS	Fetal Lung	lung
32	chr21:46221000-46222600	Active TSS	Gastric	stomach
33	chr21:46221000-46222600	Active TSS	Ovary	ovary
34	chr21:46221000-46222600	Active TSS	HMEC	breast
35	chr21:46221000-46222600	Active TSS	NHDF-Ad	bronchial
36	chr21:46221200-46222600	Active TSS	Osteobl	bone
37	chr21:46221800-46222800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr21:46222000-46222600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr21:46222000-46222800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr21:46222000-46222800	Flanking Active TSS	Fetal Muscle Trunk	muscle
41	chr21:46222200-46222600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr21:46222200-46222600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr21:46222200-46222600	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr21:46222200-46222600	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr21:46222200-46222600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr21:46222200-46222600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr21:46222200-46222600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr21:46222200-46222600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr21:46222200-46222600	Flanking Active TSS	Liver	Liver
50	chr21:46222200-46222600	Flanking Active TSS	Brain Angular Gyrus	brain

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