Variant report

Variant	rs619484
Chromosome Location	chr21:44783957-44783958
allele	C/T
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	USF2	chr21:44783903-44784190	HepG2	liver:	n/a	n/a
2	CEBPB	chr21:44783758-44784131	HepG2	liver:	n/a	chr21:44783942-44783953
3	CEBPB	chr21:44783780-44784120	IMR90	lung:	n/a	chr21:44783942-44783953
4	CEBPB	chr21:44783770-44784045	A549	lung:	n/a	chr21:44783942-44783953
5	CEBPB	chr21:44783821-44784020	HepG2	liver:	n/a	chr21:44783942-44783953
6	CEBPB	chr21:44783786-44784104	K562	blood:	n/a	chr21:44783942-44783953
7	CEBPB	chr21:44783847-44784047	Hela-S3	cervix:	n/a	chr21:44783942-44783953
8	MAX	chr21:44783907-44784093	HepG2	liver:	n/a	n/a
9	CEBPB	chr21:44783897-44783991	H1-hESC	embryonic stem cell:	n/a	chr21:44783942-44783953
10	USF1	chr21:44783915-44784142	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CRYAA-2	chr21:44783212-44785567	XLOC_013961

Variant related genes	Relation type
ENSG00000237989	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1785433	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs481767	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs504285	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.98[ASN][1000 genomes]
rs504313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525548	1.00[MEX][hapmap]
rs539072	0.98[ASN][1000 genomes]
rs573283	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs573544	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs590221	0.98[ASN][1000 genomes]
rs607398	0.88[ASN][1000 genomes]
rs621371	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633644	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs653435	0.85[ASN][1000 genomes]
rs668058	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[ASN][1000 genomes]
rs681210	0.90[MEX][hapmap]
rs8131841	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs857568	0.86[ASN][1000 genomes]
rs857572	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv913842	chr21:44764895-44792929	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs619484	LOC284837	cis	parietal	SCAN
rs619484	WRB	cis	cerebellum	SCAN
rs619484	NCRNA00257	cis	parietal	SCAN
rs619484	ERG	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44777400-44788600	Enhancers	Fetal Brain Male	brain
2	chr21:44780200-44788400	Enhancers	Spleen	Spleen
3	chr21:44780800-44784800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr21:44781000-44784800	Weak transcription	Gastric	stomach
5	chr21:44781200-44784000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr21:44781400-44785400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr21:44782200-44784000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr21:44782200-44791600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr21:44782400-44784400	Enhancers	Lung	lung
10	chr21:44782400-44784800	Weak transcription	Colonic Mucosa	Colon
11	chr21:44782400-44785000	Weak transcription	Pancreas	Pancrea
12	chr21:44782400-44785000	Weak transcription	Right Atrium	heart
13	chr21:44782400-44785400	Enhancers	Fetal Thymus	thymus
14	chr21:44782400-44789800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr21:44782600-44784800	Weak transcription	Fetal Intestine Large	intestine
16	chr21:44782600-44785200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr21:44782600-44785200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr21:44782600-44785600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr21:44782600-44785600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr21:44782600-44785600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr21:44782600-44785800	Enhancers	Fetal Brain Female	brain
22	chr21:44782600-44787000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr21:44782600-44787000	Weak transcription	Brain Substantia Nigra	brain
24	chr21:44782600-44787800	Enhancers	Fetal Muscle Leg	muscle
25	chr21:44782600-44788800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr21:44782600-44790400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr21:44782800-44784000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr21:44782800-44784200	Enhancers	Primary B cells from peripheral blood	blood
29	chr21:44782800-44784400	Weak transcription	Fetal Heart	heart
30	chr21:44782800-44784600	Weak transcription	Right Ventricle	heart
31	chr21:44782800-44785400	Weak transcription	Brain Hippocampus Middle	brain
32	chr21:44782800-44785600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr21:44782800-44787200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr21:44782800-44788600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr21:44782800-44790000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr21:44783000-44784200	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr21:44783000-44785000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr21:44783000-44785200	Weak transcription	Left Ventricle	heart
39	chr21:44783000-44785400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr21:44783000-44786000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr21:44783000-44788800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr21:44783000-44789000	Weak transcription	HMEC	breast
43	chr21:44783000-44790000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr21:44783200-44784800	Enhancers	Dnd41	blood
45	chr21:44783200-44785400	Weak transcription	Brain Anterior Caudate	brain
46	chr21:44783200-44785600	Weak transcription	Brain Angular Gyrus	brain
47	chr21:44783200-44786800	Weak transcription	Fetal Lung	lung
48	chr21:44783400-44784000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr21:44783400-44786200	Enhancers	Fetal Intestine Small	intestine
50	chr21:44783400-44788600	Weak transcription	Esophagus	oesophagus

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