Variant report

Variant	rs12894822
Chromosome Location	chr14:69532391-69532392
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:69527620..69530017-chr14:69530767..69532829,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10083451	0.83[GIH][hapmap]
rs10130013	0.83[GIH][hapmap]
rs10139873	0.83[GIH][hapmap]
rs10143302	0.83[GIH][hapmap]
rs10147369	0.83[GIH][hapmap]
rs11158782	0.83[GIH][hapmap]
rs11158787	0.83[GIH][hapmap]
rs11158790	0.83[GIH][hapmap]
rs11158795	0.80[GIH][hapmap]
rs11622889	0.81[GIH][hapmap]
rs11628353	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12431846	0.85[GIH][hapmap]
rs12432046	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12432645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12434775	0.85[GIH][hapmap]
rs12435594	0.83[GIH][hapmap]
rs12586650	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12587583	1.00[ASW][hapmap];0.90[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12589028	0.83[GIH][hapmap]
rs12884238	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs12889047	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17758220	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2001998	0.83[GIH][hapmap]
rs2056153	0.83[GIH][hapmap]
rs28613298	0.83[GIH][hapmap]
rs34075727	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34227963	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34471700	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35286356	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35700516	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36114431	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7150412	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7151437	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7157918	0.82[CHB][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AFR][1000 genomes]
rs8008184	0.83[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832823	chr14:69388853-69567638	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12894822	SPTB	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69516200-69541800	Strong transcription	Primary T cells from cord blood	blood
2	chr14:69518000-69533800	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr14:69518400-69557200	Weak transcription	Hela-S3	cervix
4	chr14:69518800-69537000	Strong transcription	Fetal Muscle Trunk	muscle
5	chr14:69519000-69537000	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr14:69519000-69537200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr14:69519200-69544600	Weak transcription	Stomach Mucosa	stomach
8	chr14:69519400-69534200	Strong transcription	Primary B cells from cord blood	blood
9	chr14:69519600-69546000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr14:69520000-69534800	Strong transcription	Placenta	Placenta
11	chr14:69521000-69540600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr14:69522200-69539600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr14:69522400-69556400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:69522400-69564800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr14:69522600-69545600	Weak transcription	Pancreas	Pancrea
16	chr14:69523400-69535600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr14:69523400-69535800	Weak transcription	Aorta	Aorta
18	chr14:69523600-69535400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr14:69523600-69545600	Weak transcription	Right Ventricle	heart
20	chr14:69523600-69550800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr14:69523600-69553400	Weak transcription	Brain Angular Gyrus	brain
22	chr14:69523600-69556400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr14:69523800-69535800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr14:69524000-69557600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr14:69524800-69556600	Weak transcription	Fetal Brain Male	brain
26	chr14:69525800-69534400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr14:69526000-69532400	Strong transcription	GM12878-XiMat	blood
28	chr14:69526200-69532600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr14:69526800-69545600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr14:69527000-69535600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr14:69527000-69545800	Weak transcription	Psoas Muscle	Psoas
32	chr14:69527000-69558200	Weak transcription	Esophagus	oesophagus
33	chr14:69527200-69535000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr14:69527200-69535400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr14:69527200-69535600	Weak transcription	HUVEC	blood vessel
36	chr14:69527400-69535600	Weak transcription	NHLF	lung
37	chr14:69527600-69532600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr14:69528000-69536200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr14:69528200-69533600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr14:69528200-69539600	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr14:69528600-69534600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr14:69528600-69535600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr14:69528600-69535800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr14:69528600-69539200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr14:69528600-69540200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr14:69528600-69545400	Weak transcription	Gastric	stomach
47	chr14:69528600-69547000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr14:69528600-69547800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr14:69528600-69550600	Weak transcription	Spleen	Spleen
50	chr14:69528600-69560200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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