Variant report

Variant	rs2823482
Chromosome Location	chr21:17145011-17145012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:17110916..17112598-chr21:17143499..17145312,2	K562	blood:
2	chr21:17141263..17145457-chr21:17148743..17151657,3	MCF-7	breast:
3	chr21:17123698..17126562-chr21:17142609..17145221,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11910884	0.88[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs11911814	0.85[ASN][1000 genomes]
rs1989381	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2026853	0.83[ASW][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs2205585	0.90[AFR][1000 genomes]
rs2205589	0.83[AFR][1000 genomes]
rs2223176	0.90[AFR][1000 genomes]
rs2245574	0.88[CHB][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs2823469	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2823470	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2823472	0.88[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2823476	0.97[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2823477	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs2823481	1.00[CEU][hapmap]
rs2823487	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs2823488	0.81[AFR][1000 genomes]
rs2823489	0.94[CHB][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2823493	0.88[CHB][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs2823495	0.87[AFR][1000 genomes]
rs2823496	0.90[AFR][1000 genomes]
rs2823497	0.88[AFR][1000 genomes]
rs2823499	0.88[CHB][hapmap];0.87[CHD][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs2823500	0.94[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs28725201	0.88[ASN][1000 genomes]
rs6517609	0.88[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6517611	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6517612	0.81[LWK][hapmap];0.91[MEX][hapmap];0.86[YRI][hapmap]
rs6517613	0.82[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6517648	0.89[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6517652	0.89[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs722887	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7279157	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7279170	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7281511	0.90[YRI][hapmap]
rs7283707	0.89[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs73346766	0.84[AFR][1000 genomes]
rs8127158	0.82[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs8130607	0.81[LWK][hapmap];0.91[MEX][hapmap];0.86[YRI][hapmap]
rs8134327	0.89[ASW][hapmap];0.82[CHB][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs926612	0.91[MEX][hapmap]
rs9941829	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9974210	0.88[AFR][1000 genomes]
rs9976815	0.84[AFR][1000 genomes]
rs9977000	0.88[AFR][1000 genomes]
rs9981766	0.90[AFR][1000 genomes]
rs9982083	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9982479	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9983248	0.82[AFR][1000 genomes]
rs9983458	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762093	chr21:16948663-17145770	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1064683	chr21:16954570-17145758	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv459099	chr21:16956866-17145011	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv587076	chr21:16956866-17145011	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1059500	chr21:16957752-17145758	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv1815433	chr21:17106192-17167353	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2823482	MSX1	trans	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17115400-17145400	Weak transcription	Fetal Thymus	thymus
2	chr21:17116600-17145400	Weak transcription	Esophagus	oesophagus
3	chr21:17125800-17153400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr21:17126800-17147600	Weak transcription	Placenta	Placenta
5	chr21:17127000-17147400	Weak transcription	HSMMtube	muscle
6	chr21:17127000-17152800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr21:17127200-17153400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr21:17127400-17146200	Weak transcription	NHDF-Ad	bronchial
9	chr21:17127400-17147800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr21:17127400-17153400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr21:17127600-17145200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr21:17127800-17152800	Weak transcription	Fetal Intestine Large	intestine
13	chr21:17130800-17156800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr21:17132800-17153400	Weak transcription	Spleen	Spleen
15	chr21:17133800-17145800	Weak transcription	Colon Smooth Muscle	Colon
16	chr21:17133800-17149400	Weak transcription	Small Intestine	intestine
17	chr21:17134000-17147600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr21:17134000-17152400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr21:17134000-17153400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr21:17134200-17153000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr21:17134200-17153400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr21:17134200-17154000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr21:17134400-17153200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr21:17135000-17152600	Weak transcription	Primary T cells from cord blood	blood
25	chr21:17135000-17153000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr21:17135000-17153400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr21:17135000-17153600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr21:17135200-17153000	Weak transcription	Fetal Muscle Leg	muscle
29	chr21:17135400-17153200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr21:17135600-17153200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr21:17135800-17147200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr21:17136000-17145400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr21:17136600-17148400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr21:17136600-17153200	Weak transcription	Thymus	Thymus
35	chr21:17137600-17145400	Weak transcription	Fetal Stomach	stomach
36	chr21:17138600-17152800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr21:17139200-17146200	Weak transcription	NHLF	lung
38	chr21:17139600-17145200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr21:17139600-17145400	Weak transcription	Fetal Intestine Small	intestine
40	chr21:17139600-17150800	Weak transcription	Fetal Kidney	kidney
41	chr21:17139800-17145400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr21:17139800-17149000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr21:17139800-17153000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr21:17139800-17153400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr21:17139800-17153400	Weak transcription	Aorta	Aorta
46	chr21:17140000-17145400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr21:17140000-17146200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr21:17140000-17149000	Weak transcription	Liver	Liver
49	chr21:17140000-17152800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr21:17140200-17150800	Weak transcription	Fetal Lung	lung

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