Variant report

Variant	rs12891828
Chromosome Location	chr14:81654524-81654525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:81653722..81660939-chr14:81683638..81690429,10	MCF-7	breast:
2	chr14:81643246..81655314-chr14:81683241..81689401,24	K562	blood:
3	chr14:81649228..81655392-chr14:81682762..81688409,10	K562	blood:
4	chr14:81654146..81656422-chr14:81667896..81670751,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165417	Chromatin interaction
ENSG00000221303	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10131728	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878339	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878477	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12878503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12879576	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12880377	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12880414	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12880512	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12880551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap]
rs12883359	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12883532	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12889291	1.00[CHB][hapmap]
rs12891586	0.85[AMR][1000 genomes]
rs12892815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes]
rs12892839	0.85[AMR][1000 genomes]
rs12893275	0.85[CEU][hapmap]
rs12893436	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12894001	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12894318	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12894596	1.00[CHB][hapmap]
rs12895215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[TSI][hapmap]
rs12895990	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17630746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35446669	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4592586	0.88[AMR][1000 genomes];1.00[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	nsv832841	chr14:81588322-81743921	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	86 gene(s)	inside rSNPs	diseases
2	nsv902117	chr14:81643800-81682392	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12891828	TBC1D30	trans	lymphoblastoid	seeQTL
rs12891828	GBP6	trans	lymphoblastoid	seeQTL
rs12891828	NRXN3	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:81637000-81659000	Weak transcription	Esophagus	oesophagus
2	chr14:81637000-81683800	Weak transcription	Small Intestine	intestine
3	chr14:81637200-81658200	Weak transcription	HSMMtube	muscle
4	chr14:81637200-81658800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr14:81637200-81658800	Weak transcription	Colonic Mucosa	Colon
6	chr14:81637200-81658800	Weak transcription	Left Ventricle	heart
7	chr14:81637400-81656800	Weak transcription	HMEC	breast
8	chr14:81637400-81658800	Weak transcription	Fetal Brain Male	brain
9	chr14:81637400-81659000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr14:81638600-81670200	Weak transcription	Psoas Muscle	Psoas
11	chr14:81640000-81657200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr14:81640000-81658800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr14:81642400-81658800	Weak transcription	Pancreas	Pancrea
14	chr14:81643600-81658800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr14:81643800-81683200	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr14:81644000-81655400	Strong transcription	Dnd41	blood
17	chr14:81644200-81658400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr14:81644200-81683600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr14:81644600-81655400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr14:81644600-81658200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr14:81644600-81658600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr14:81644600-81658800	Weak transcription	Brain Angular Gyrus	brain
23	chr14:81644600-81666400	Weak transcription	Stomach Mucosa	stomach
24	chr14:81644600-81685400	Weak transcription	Right Ventricle	heart
25	chr14:81644800-81675600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:81645000-81658800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr14:81645200-81655000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr14:81645600-81654800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr14:81646000-81664800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr14:81646200-81674800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr14:81646800-81654600	Strong transcription	Primary B cells from cord blood	blood
32	chr14:81647200-81664600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr14:81647200-81674400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr14:81647400-81674600	Strong transcription	Primary B cells from peripheral blood	blood
35	chr14:81647600-81656200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr14:81648000-81655400	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr14:81648000-81671400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr14:81648600-81662200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr14:81648800-81667800	Weak transcription	Fetal Heart	heart
40	chr14:81649000-81660400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr14:81649200-81656200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr14:81649200-81656600	Weak transcription	NHDF-Ad	bronchial
43	chr14:81649200-81657200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr14:81649200-81659000	Weak transcription	Brain Substantia Nigra	brain
45	chr14:81649200-81660400	Weak transcription	Brain Hippocampus Middle	brain
46	chr14:81649200-81677800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr14:81649400-81657600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr14:81649400-81658800	Weak transcription	Lung	lung
49	chr14:81649400-81660400	Weak transcription	Aorta	Aorta
50	chr14:81649600-81658800	Weak transcription	Brain Anterior Caudate	brain

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