Variant report

Variant	rs634978
Chromosome Location	chr21:44782732-44782733
allele	A/C/G/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	MTA3	chr21:44782045-44782815	GM12878	blood:	n/a	n/a
2	POLR2A	chr21:44782061-44782821	SK-N-MC	brain:	n/a	n/a
3	EP300	chr21:44781956-44782950	SK-N-SH	brain:	n/a	chr21:44782350-44782366
4	JUN	chr21:44782689-44783298	K562	blood:	n/a	chr21:44782714-44782723
5	BHLHE40	chr21:44782215-44783208	GM12878	blood:	n/a	n/a
6	MXI1	chr21:44781973-44782929	SK-N-SH	brain:	n/a	n/a
7	MAZ	chr21:44780514-44782772	IMR90	lung:	n/a	n/a
8	STAT3	chr21:44782637-44782779	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:44781136..44783679-chr21:44846485..44848438,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225637	TF binding region
ENSG00000237989	TF binding region
ENSG00000142178	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs496300	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs554253	0.88[EUR][1000 genomes]
rs559480	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs559652	0.87[EUR][1000 genomes]
rs564779	0.87[TSI][hapmap]
rs565629	0.87[TSI][hapmap]
rs579870	0.81[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs672929	0.81[TSI][hapmap]
rs672948	0.96[CEU][hapmap];0.86[CHB][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs857569	0.87[TSI][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs634978	WRB	cis	cerebellum	SCAN
rs634978	NCRNA00257	cis	parietal	SCAN
rs634978	C21orf2	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44777400-44788600	Enhancers	Fetal Brain Male	brain
2	chr21:44780000-44783600	Enhancers	Primary B cells from cord blood	blood
3	chr21:44780200-44788400	Enhancers	Spleen	Spleen
4	chr21:44780600-44782800	Enhancers	Fetal Heart	heart
5	chr21:44780800-44783000	Bivalent Enhancer	Fetal Stomach	stomach
6	chr21:44780800-44783200	Flanking Active TSS	Dnd41	blood
7	chr21:44780800-44784800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr21:44781000-44782800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr21:44781000-44782800	Flanking Active TSS	GM12878-XiMat	blood
10	chr21:44781000-44783000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr21:44781000-44784800	Weak transcription	Gastric	stomach
12	chr21:44781200-44782800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr21:44781200-44782800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
14	chr21:44781200-44782800	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr21:44781200-44782800	Enhancers	Brain Hippocampus Middle	brain
16	chr21:44781200-44782800	Enhancers	NH-A	brain
17	chr21:44781200-44783800	Enhancers	Primary hematopoietic stem cells	blood
18	chr21:44781200-44784000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr21:44781400-44782800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr21:44781400-44782800	Active TSS	Rectal Smooth Muscle	rectum
21	chr21:44781400-44783000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr21:44781400-44783200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr21:44781400-44783600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr21:44781400-44785400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr21:44781600-44782800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr21:44781600-44783000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
27	chr21:44781600-44783400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr21:44781800-44782800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr21:44781800-44782800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr21:44781800-44782800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr21:44781800-44783000	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr21:44781800-44783000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr21:44781800-44783000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr21:44782000-44782800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr21:44782000-44782800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
36	chr21:44782000-44783000	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr21:44782000-44783000	Enhancers	HUVEC	blood vessel
38	chr21:44782000-44783200	Enhancers	Brain Angular Gyrus	brain
39	chr21:44782000-44783800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr21:44782000-44783800	Enhancers	HSMMtube	muscle
41	chr21:44782200-44782800	Enhancers	H9 Cell Line	embryonic stem cell
42	chr21:44782200-44782800	Active TSS	Colon Smooth Muscle	Colon
43	chr21:44782200-44782800	Enhancers	Right Ventricle	heart
44	chr21:44782200-44783000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr21:44782200-44783000	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr21:44782200-44783000	Enhancers	NHLF	lung
47	chr21:44782200-44783400	Enhancers	Fetal Muscle Trunk	muscle
48	chr21:44782200-44783600	Bivalent Enhancer	Placenta	Placenta
49	chr21:44782200-44783800	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr21:44782200-44784000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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