Variant report

Variant	rs2823504
Chromosome Location	chr21:17207648-17207649
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:17204554..17207689-chr21:17213044..17215185,3	K562	blood:

Variant related genes	Relation type
ENSG00000155313	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1022457	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10482876	0.91[CEU][hapmap]
rs11910884	0.90[CEU][hapmap]
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	0.91[CEU][hapmap]
rs2242676	0.91[CEU][hapmap]
rs2245574	0.82[CEU][hapmap]
rs2404001	0.91[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs2823454	0.88[JPT][hapmap];0.94[YRI][hapmap]
rs2823455	0.82[CEU][hapmap]
rs2823471	0.91[CEU][hapmap]
rs2823472	0.91[CEU][hapmap]
rs2823478	0.91[CEU][hapmap]
rs2823489	0.91[CEU][hapmap]
rs2823491	0.91[CEU][hapmap]
rs2823493	0.91[CEU][hapmap]
rs2823499	0.91[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs2823500	0.91[CEU][hapmap]
rs2823502	0.99[ASN][1000 genomes]
rs2823503	0.99[ASN][1000 genomes]
rs2823505	0.81[EUR][1000 genomes]
rs2823507	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2823510	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2823511	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2823513	0.94[EUR][1000 genomes]
rs2823517	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2823518	0.87[EUR][1000 genomes]
rs28469763	0.83[ASN][1000 genomes]
rs3787577	0.91[CEU][hapmap]
rs392203	0.89[ASN][1000 genomes]
rs463566	0.84[CEU][hapmap]
rs6517609	0.91[CEU][hapmap]
rs6517613	0.91[CEU][hapmap]
rs6517648	0.91[CEU][hapmap]
rs6517652	0.91[CEU][hapmap]
rs6517675	0.81[EUR][1000 genomes]
rs7278727	0.84[EUR][1000 genomes]
rs7281511	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs7283707	0.91[CEU][hapmap]
rs73346766	0.81[EUR][1000 genomes]
rs8127158	0.91[CEU][hapmap]
rs8127570	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127734	0.92[ASN][1000 genomes]
rs8128766	0.81[EUR][1000 genomes]
rs8134327	0.82[CEU][hapmap]
rs97928	0.88[JPT][hapmap]
rs9974210	0.81[EUR][1000 genomes]
rs9980260	0.89[ASN][1000 genomes]
rs9983248	0.81[EUR][1000 genomes]
rs9983385	0.81[EUR][1000 genomes]
rs9983858	0.81[EUR][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
rs2823504	TACC2	cis	Temporal Cortex	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17155200-17209800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr21:17155200-17252800	Weak transcription	Fetal Brain Male	brain
3	chr21:17177200-17208800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr21:17178400-17248200	Weak transcription	Esophagus	oesophagus
5	chr21:17178400-17252800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr21:17178800-17211400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr21:17182400-17227800	Weak transcription	Psoas Muscle	Psoas
8	chr21:17184000-17209800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr21:17187400-17208800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr21:17188000-17208800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr21:17188000-17214000	Weak transcription	Gastric	stomach
12	chr21:17188000-17229400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr21:17188000-17240200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr21:17188200-17213400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr21:17188200-17246800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr21:17188400-17247200	Weak transcription	Ovary	ovary
17	chr21:17188400-17253200	Weak transcription	Fetal Brain Female	brain
18	chr21:17188600-17210000	Weak transcription	Aorta	Aorta
19	chr21:17188600-17210400	Weak transcription	Fetal Intestine Small	intestine
20	chr21:17188600-17213400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr21:17188800-17247000	Weak transcription	Brain Germinal Matrix	brain
22	chr21:17188800-17252600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr21:17190200-17245400	Weak transcription	Lung	lung
24	chr21:17190200-17247200	Weak transcription	Pancreas	Pancrea
25	chr21:17190400-17247200	Weak transcription	Spleen	Spleen
26	chr21:17190400-17247400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr21:17191000-17227800	Weak transcription	Colonic Mucosa	Colon
28	chr21:17191800-17211600	Weak transcription	NH-A	brain
29	chr21:17191800-17212800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr21:17194000-17209600	Weak transcription	Osteobl	bone
31	chr21:17194200-17228000	Weak transcription	Small Intestine	intestine
32	chr21:17194800-17218000	Weak transcription	Hela-S3	cervix
33	chr21:17197000-17208000	Strong transcription	Dnd41	blood
34	chr21:17197200-17208000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr21:17197200-17218400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr21:17197800-17208000	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr21:17198000-17214200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr21:17198000-17248000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr21:17198400-17208400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr21:17198600-17208800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr21:17198800-17208400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr21:17199200-17208800	Strong transcription	Liver	Liver
43	chr21:17199400-17218800	Weak transcription	Right Ventricle	heart
44	chr21:17199600-17209600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr21:17199600-17210200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr21:17199600-17213200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr21:17199800-17214200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr21:17199800-17246800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr21:17199800-17247200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr21:17200000-17211800	Weak transcription	NHEK	skin

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