Variant report

Variant	rs1338905
Chromosome Location	chr6:131361935-131361936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:131356533..131360824-chr6:131360872..131363958,3	MCF-7	breast:
2	chr6:131361605..131363567-chr6:131382712..131384609,2	MCF-7	breast:
3	chr6:131356781..131360402-chr6:131360756..131363630,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079819	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10499174	0.92[JPT][hapmap]
rs12661081	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12664355	0.87[CHD][hapmap];0.92[JPT][hapmap]
rs13193246	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1332490	0.89[CEU][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1332491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17059681	0.87[CHD][hapmap];0.92[JPT][hapmap]
rs17059683	0.92[JPT][hapmap]
rs17059698	0.92[JPT][hapmap]
rs17059702	0.92[JPT][hapmap]
rs17059896	0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs17059925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17831009	0.92[JPT][hapmap]
rs1855077	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1888959	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1976982	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2007339	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2151069	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2225557	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2275063	0.92[JPT][hapmap]
rs2275065	0.81[ASN][1000 genomes]
rs3777450	0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs3777453	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs3777463	0.88[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs3822864	0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs4895902	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4897480	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897481	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897482	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897488	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4897490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56027377	0.81[ASN][1000 genomes]
rs6569716	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6569718	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6569722	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6569725	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6900810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908917	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6909134	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6928986	0.89[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6942081	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73623428	0.99[ASN][1000 genomes]
rs73774307	0.81[ASN][1000 genomes]
rs73774328	0.91[ASN][1000 genomes]
rs7742376	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7747881	0.88[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs7765007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7765757	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769153	0.88[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs9321268	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9372988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9689026	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1338905	AKAP7	cis	multi-tissue	Pritchard

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131346000-131375000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:131351400-131375000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:131351600-131374600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:131352400-131374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:131353800-131364000	Weak transcription	Ovary	ovary
6	chr6:131356600-131375000	Weak transcription	Brain Angular Gyrus	brain
7	chr6:131357400-131367200	Weak transcription	Fetal Intestine Small	intestine
8	chr6:131359000-131374800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:131360400-131365600	Weak transcription	Adipose Nuclei	Adipose
10	chr6:131360400-131367400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:131360600-131362200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:131360600-131362800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:131360600-131363400	Weak transcription	A549	lung
14	chr6:131360600-131367200	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:131360800-131362000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:131360800-131362000	Weak transcription	Brain Anterior Caudate	brain
17	chr6:131360800-131362400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:131360800-131363200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:131360800-131364000	Enhancers	NHLF	lung
20	chr6:131360800-131364800	Enhancers	HepG2	liver
21	chr6:131360800-131368000	Weak transcription	Small Intestine	intestine
22	chr6:131360800-131370000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:131360800-131374800	Weak transcription	HSMM	muscle
24	chr6:131360800-131375000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:131361000-131362000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:131361000-131362000	Weak transcription	NHDF-Ad	bronchial
27	chr6:131361000-131362000	Weak transcription	Osteobl	bone
28	chr6:131361000-131362800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:131361000-131367600	Weak transcription	Brain Substantia Nigra	brain
30	chr6:131361200-131362200	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:131361400-131362200	Weak transcription	Fetal Stomach	stomach
32	chr6:131361400-131373800	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:131361600-131369000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:131361800-131362600	Enhancers	Fetal Lung	lung

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