Variant report

Variant	rs2823502
Chromosome Location	chr21:17202780-17202781
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1022457	0.92[ASN][1000 genomes]
rs10482876	0.91[CEU][hapmap]
rs11909953	0.83[YRI][hapmap]
rs11910884	0.90[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs1543299	0.82[CEU][hapmap]
rs17241416	0.91[CEU][hapmap]
rs17241423	0.89[CEU][hapmap]
rs17241430	0.91[CEU][hapmap]
rs17241444	0.91[CEU][hapmap]
rs17307176	0.91[CEU][hapmap]
rs2026853	1.00[ASW][hapmap];0.91[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs2205585	0.88[AFR][1000 genomes]
rs2205589	0.92[AFR][1000 genomes]
rs2223176	0.88[AFR][1000 genomes]
rs2242676	0.91[CEU][hapmap]
rs2245574	0.82[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs2252133	0.98[EUR][1000 genomes]
rs2404001	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs2823454	0.88[JPT][hapmap]
rs2823455	0.82[CEU][hapmap]
rs2823471	0.91[CEU][hapmap]
rs2823472	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs2823477	0.86[YRI][hapmap]
rs2823478	0.91[CEU][hapmap]
rs2823482	0.81[ASW][hapmap];0.93[YRI][hapmap]
rs2823487	0.82[YRI][hapmap]
rs2823489	0.91[CEU][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs2823491	0.91[CEU][hapmap]
rs2823493	0.91[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs2823495	0.86[AFR][1000 genomes]
rs2823496	0.88[AFR][1000 genomes]
rs2823497	0.91[AFR][1000 genomes]
rs2823499	0.93[ASW][hapmap];0.91[CEU][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs2823500	0.91[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs2823503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823504	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2823505	0.88[AFR][1000 genomes]
rs2823507	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2823509	0.98[EUR][1000 genomes]
rs2823510	0.92[ASN][1000 genomes]
rs2823511	0.92[ASN][1000 genomes]
rs2823516	0.94[EUR][1000 genomes]
rs2823517	0.91[ASN][1000 genomes]
rs28469763	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28679848	0.87[EUR][1000 genomes]
rs3787577	0.91[CEU][hapmap]
rs392203	0.88[ASN][1000 genomes]
rs6517609	0.91[CEU][hapmap];0.93[YRI][hapmap]
rs6517612	0.87[ASW][hapmap];0.83[YRI][hapmap]
rs6517613	0.91[CEU][hapmap];0.93[YRI][hapmap]
rs6517648	0.93[ASW][hapmap];0.91[CEU][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs6517652	0.93[ASW][hapmap];0.91[CEU][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs6517675	0.88[AFR][1000 genomes]
rs7278727	0.90[AFR][1000 genomes]
rs7281511	0.91[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs7283467	0.91[EUR][1000 genomes]
rs7283707	0.93[ASW][hapmap];0.91[CEU][hapmap];0.93[YRI][hapmap]
rs7283839	0.83[AFR][1000 genomes]
rs73346766	0.87[AFR][1000 genomes]
rs8127158	0.91[CEU][hapmap];0.93[YRI][hapmap]
rs8127570	0.99[ASN][1000 genomes]
rs8127734	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8128766	0.88[AFR][1000 genomes]
rs8130607	0.87[ASW][hapmap];0.83[YRI][hapmap]
rs8134327	0.93[ASW][hapmap];0.82[CEU][hapmap];0.93[YRI][hapmap]
rs97928	0.88[JPT][hapmap]
rs9974210	0.91[AFR][1000 genomes]
rs9976815	0.87[AFR][1000 genomes]
rs9977000	0.91[AFR][1000 genomes]
rs9977069	0.88[AFR][1000 genomes]
rs9980260	0.88[ASN][1000 genomes]
rs9981766	0.90[AFR][1000 genomes]
rs9983248	0.87[AFR][1000 genomes]
rs9983385	0.86[AFR][1000 genomes]
rs9983858	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834050	chr21:17146090-17348951	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv1063035	chr21:17154222-17224344	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2823502	TACC2	cis	Temporal Cortex	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17155200-17203800	Weak transcription	Colon Smooth Muscle	Colon
2	chr21:17155200-17209800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr21:17155200-17252800	Weak transcription	Fetal Brain Male	brain
4	chr21:17177200-17208800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr21:17178400-17248200	Weak transcription	Esophagus	oesophagus
6	chr21:17178400-17252800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr21:17178800-17211400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr21:17182400-17227800	Weak transcription	Psoas Muscle	Psoas
9	chr21:17184000-17203800	Weak transcription	Brain Hippocampus Middle	brain
10	chr21:17184000-17209800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr21:17186200-17204200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr21:17187400-17208800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr21:17187800-17203600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr21:17188000-17203800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr21:17188000-17208800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr21:17188000-17214000	Weak transcription	Gastric	stomach
17	chr21:17188000-17229400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr21:17188000-17240200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr21:17188200-17203800	Weak transcription	Fetal Lung	lung
20	chr21:17188200-17213400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr21:17188200-17246800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr21:17188400-17206600	Weak transcription	Stomach Mucosa	stomach
23	chr21:17188400-17247200	Weak transcription	Ovary	ovary
24	chr21:17188400-17253200	Weak transcription	Fetal Brain Female	brain
25	chr21:17188600-17210000	Weak transcription	Aorta	Aorta
26	chr21:17188600-17210400	Weak transcription	Fetal Intestine Small	intestine
27	chr21:17188600-17213400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr21:17188800-17206400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr21:17188800-17247000	Weak transcription	Brain Germinal Matrix	brain
30	chr21:17188800-17252600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr21:17189000-17203000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr21:17190200-17203800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr21:17190200-17245400	Weak transcription	Lung	lung
34	chr21:17190200-17247200	Weak transcription	Pancreas	Pancrea
35	chr21:17190400-17203800	Weak transcription	Brain Angular Gyrus	brain
36	chr21:17190400-17247200	Weak transcription	Spleen	Spleen
37	chr21:17190400-17247400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr21:17190600-17203600	Weak transcription	Thymus	Thymus
39	chr21:17190600-17203800	Weak transcription	Brain Anterior Caudate	brain
40	chr21:17191000-17227800	Weak transcription	Colonic Mucosa	Colon
41	chr21:17191200-17207000	Weak transcription	Left Ventricle	heart
42	chr21:17191800-17211600	Weak transcription	NH-A	brain
43	chr21:17191800-17212800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr21:17192000-17203200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr21:17192000-17203800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr21:17192400-17203400	Weak transcription	HMEC	breast
47	chr21:17194000-17209600	Weak transcription	Osteobl	bone
48	chr21:17194200-17202800	Weak transcription	NHLF	lung
49	chr21:17194200-17228000	Weak transcription	Small Intestine	intestine
50	chr21:17194800-17218000	Weak transcription	Hela-S3	cervix

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