Variant report

Variant	rs633644
Chromosome Location	chr21:44783063-44783064
allele	C/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	HDAC2	chr21:44782885-44783116	K562	blood:	n/a	n/a
2	STAT5A	chr21:44782793-44783219	K562	blood:	n/a	chr21:44783174-44783186 chr21:44782985-44782994 chr21:44782986-44782995 chr21:44782983-44782997
3	CCNT2	chr21:44782983-44783086	K562	blood:	n/a	n/a
4	YY1	chr21:44782823-44783112	GM12878	blood:	n/a	n/a
5	EP300	chr21:44782827-44783109	K562	blood:	n/a	n/a
6	JUND	chr21:44782821-44783154	K562	blood:	n/a	n/a
7	JUN	chr21:44782689-44783298	K562	blood:	n/a	chr21:44782714-44782723
8	BHLHE40	chr21:44782215-44783208	GM12878	blood:	n/a	n/a
9	TEAD4	chr21:44782738-44783251	K562	blood:	n/a	n/a
10	BHLHE40	chr21:44782818-44783103	K562	blood:	n/a	n/a
11	MYC	chr21:44782891-44783119	K562	blood:	n/a	n/a
12	TCF12	chr21:44782823-44783084	GM12878	blood:	n/a	n/a
13	RUNX3	chr21:44782754-44783184	GM12878	blood:	n/a	n/a
14	NR2F2	chr21:44782759-44783116	K562	blood:	n/a	n/a
15	STAT5A	chr21:44782797-44783172	K562	blood:	n/a	chr21:44782985-44782994 chr21:44782986-44782995 chr21:44782983-44782997
16	HDAC2	chr21:44782776-44783148	K562	blood:	n/a	n/a
17	TBL1XR1	chr21:44782949-44783109	GM12878	blood:	n/a	n/a
18	RCOR1	chr21:44782801-44783132	K562	blood:	n/a	n/a
19	RCOR1	chr21:44782771-44783187	K562	blood:	n/a	n/a
20	RUNX3	chr21:44782746-44783207	GM12878	blood:	n/a	n/a
21	EP300	chr21:44782869-44783170	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
ENSG00000237989	TF binding region
ENSG00000225637	TF binding region
ENSG00000142178	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1785433	0.96[ASN][1000 genomes]
rs481767	0.82[ASN][1000 genomes]
rs504285	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs504313	0.86[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs524850	0.80[AMR][1000 genomes]
rs525548	0.90[MEX][hapmap]
rs539072	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs573283	0.91[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs573544	0.91[CHB][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs590221	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs607398	0.89[ASN][1000 genomes]
rs619484	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs621371	0.97[ASN][1000 genomes]
rs653435	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs668058	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs681210	0.90[MEX][hapmap]
rs8131841	0.96[ASN][1000 genomes]
rs857568	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs857572	0.86[CHB][hapmap];0.87[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs633644	DSCAM	cis	cerebellum	SCAN
rs633644	C21orf29	cis	cerebellum	SCAN
rs633644	ERG	cis	cerebellum	SCAN
rs633644	WRB	cis	cerebellum	SCAN
rs633644	NCRNA00257	cis	parietal	SCAN

Chromatin state (count:79 , 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	chr21:44780800-44783200	Flanking Active TSS	Dnd41	blood
5	chr21:44780800-44784800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr21:44781000-44784800	Weak transcription	Gastric	stomach
7	chr21:44781200-44783800	Enhancers	Primary hematopoietic stem cells	blood
8	chr21:44781200-44784000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr21:44781400-44783200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr21:44781400-44783600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr21:44781400-44785400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr21:44781600-44783400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr21:44782000-44783200	Enhancers	Brain Angular Gyrus	brain
14	chr21:44782000-44783800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr21:44782000-44783800	Enhancers	HSMMtube	muscle
16	chr21:44782200-44783400	Enhancers	Fetal Muscle Trunk	muscle
17	chr21:44782200-44783600	Bivalent Enhancer	Placenta	Placenta
18	chr21:44782200-44783800	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr21:44782200-44784000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr21:44782200-44791600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr21:44782400-44783200	Enhancers	Fetal Lung	lung
22	chr21:44782400-44783600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr21:44782400-44784400	Enhancers	Lung	lung
24	chr21:44782400-44784800	Weak transcription	Colonic Mucosa	Colon
25	chr21:44782400-44785000	Weak transcription	Pancreas	Pancrea
26	chr21:44782400-44785000	Weak transcription	Right Atrium	heart
27	chr21:44782400-44785400	Enhancers	Fetal Thymus	thymus
28	chr21:44782400-44789800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr21:44782600-44783200	Bivalent Enhancer	Adipose Nuclei	Adipose
30	chr21:44782600-44783400	Enhancers	Esophagus	oesophagus
31	chr21:44782600-44783400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr21:44782600-44783400	Enhancers	Thymus	Thymus
33	chr21:44782600-44783600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr21:44782600-44783800	Enhancers	Brain Germinal Matrix	brain
35	chr21:44782600-44783800	Enhancers	HSMM	muscle
36	chr21:44782600-44784800	Weak transcription	Fetal Intestine Large	intestine
37	chr21:44782600-44785200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr21:44782600-44785200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr21:44782600-44785600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr21:44782600-44785600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr21:44782600-44785600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr21:44782600-44785800	Enhancers	Fetal Brain Female	brain
43	chr21:44782600-44787000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr21:44782600-44787000	Weak transcription	Brain Substantia Nigra	brain
45	chr21:44782600-44787800	Enhancers	Fetal Muscle Leg	muscle
46	chr21:44782600-44788800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr21:44782600-44790400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr21:44782800-44783200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr21:44782800-44783200	Enhancers	Brain Anterior Caudate	brain
50	chr21:44782800-44783200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood

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