Variant report

Variant	rs2823507
Chromosome Location	chr21:17226028-17226029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:17220358..17222293-chr21:17224213..17226942,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1022457	0.90[ASN][1000 genomes]
rs10482876	0.83[CEU][hapmap]
rs11910884	0.81[CEU][hapmap]
rs17241416	0.83[CEU][hapmap]
rs17241430	0.83[CEU][hapmap]
rs17241444	0.83[CEU][hapmap]
rs17307176	0.83[CEU][hapmap]
rs2026853	0.83[CEU][hapmap]
rs2242676	0.83[CEU][hapmap]
rs2252133	0.94[EUR][1000 genomes]
rs2404001	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs2823471	0.83[CEU][hapmap]
rs2823472	0.83[CEU][hapmap]
rs2823478	0.83[CEU][hapmap]
rs2823489	0.83[CEU][hapmap]
rs2823491	0.83[CEU][hapmap]
rs2823493	0.83[CEU][hapmap]
rs2823499	0.83[CEU][hapmap]
rs2823500	0.83[CEU][hapmap]
rs2823502	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2823503	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2823504	0.94[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2823506	0.93[ASN][1000 genomes]
rs2823509	0.94[EUR][1000 genomes]
rs2823510	0.91[ASN][1000 genomes]
rs2823511	0.91[ASN][1000 genomes]
rs2823516	0.90[EUR][1000 genomes]
rs2823517	0.89[ASN][1000 genomes]
rs28469763	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28679848	0.84[EUR][1000 genomes]
rs3787577	0.83[CEU][hapmap]
rs392203	0.84[ASN][1000 genomes]
rs460497	0.87[JPT][hapmap]
rs463566	0.87[JPT][hapmap]
rs6517609	0.83[CEU][hapmap]
rs6517613	0.83[CEU][hapmap]
rs6517648	0.83[CEU][hapmap]
rs6517652	0.83[CEU][hapmap]
rs7281511	0.83[CEU][hapmap]
rs7283467	0.88[EUR][1000 genomes]
rs7283707	0.83[CEU][hapmap]
rs8127158	0.83[CEU][hapmap]
rs8127570	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs8127734	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9980260	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][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	nsv962648	chr21:17222801-17227895	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2823507	TACC2	cis	Temporal Cortex	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17155200-17252800	Weak transcription	Fetal Brain Male	brain
2	chr21:17178400-17248200	Weak transcription	Esophagus	oesophagus
3	chr21:17178400-17252800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr21:17182400-17227800	Weak transcription	Psoas Muscle	Psoas
5	chr21:17188000-17229400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:17188000-17240200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr21:17188200-17246800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr21:17188400-17247200	Weak transcription	Ovary	ovary
9	chr21:17188400-17253200	Weak transcription	Fetal Brain Female	brain
10	chr21:17188800-17247000	Weak transcription	Brain Germinal Matrix	brain
11	chr21:17188800-17252600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr21:17190200-17245400	Weak transcription	Lung	lung
13	chr21:17190200-17247200	Weak transcription	Pancreas	Pancrea
14	chr21:17190400-17247200	Weak transcription	Spleen	Spleen
15	chr21:17190400-17247400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr21:17191000-17227800	Weak transcription	Colonic Mucosa	Colon
17	chr21:17194200-17228000	Weak transcription	Small Intestine	intestine
18	chr21:17198000-17248000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr21:17199800-17246800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr21:17199800-17247200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr21:17200800-17245200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr21:17201200-17230200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr21:17201400-17245400	Weak transcription	Fetal Stomach	stomach
24	chr21:17204400-17239000	Weak transcription	Brain Substantia Nigra	brain
25	chr21:17204400-17246400	Weak transcription	Brain Angular Gyrus	brain
26	chr21:17204400-17246800	Weak transcription	Brain Anterior Caudate	brain
27	chr21:17204600-17229200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr21:17204600-17230200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr21:17204600-17247800	Weak transcription	HepG2	liver
30	chr21:17204600-17252800	Weak transcription	Brain Hippocampus Middle	brain
31	chr21:17207600-17229600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr21:17210400-17228600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr21:17210400-17252600	Weak transcription	Aorta	Aorta
34	chr21:17210600-17239000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr21:17210600-17245400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr21:17210600-17247200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr21:17211000-17245400	Weak transcription	Fetal Intestine Small	intestine
38	chr21:17211000-17246600	Weak transcription	Colon Smooth Muscle	Colon
39	chr21:17211600-17227800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr21:17213600-17227800	Weak transcription	GM12878-XiMat	blood
41	chr21:17214200-17245400	Weak transcription	Gastric	stomach
42	chr21:17214600-17237800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr21:17215000-17226600	Weak transcription	Primary T cells from cord blood	blood
44	chr21:17215000-17236600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr21:17215000-17240600	Weak transcription	Fetal Muscle Leg	muscle
46	chr21:17215000-17240600	Weak transcription	HSMMtube	muscle
47	chr21:17215000-17245200	Weak transcription	Fetal Kidney	kidney
48	chr21:17215000-17245400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr21:17215200-17226400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr21:17215200-17226800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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