Variant report

Variant	rs6496877
Chromosome Location	chr15:92477919-92477920
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:92461295..92463798-chr15:92477370..92479994,2	K562	blood:
2	chr15:92467181..92469484-chr15:92477691..92480563,2	MCF-7	breast:
3	chr15:92477044..92480938-chr15:92480980..92485155,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176463	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10444871	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12901800	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4077721	0.81[JPT][hapmap]
rs4244911	0.96[CEU][hapmap]
rs4294800	0.81[JPT][hapmap]
rs4420511	0.84[EUR][1000 genomes]
rs4932515	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs4932518	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6496870	0.81[JPT][hapmap]
rs6496874	0.81[JPT][hapmap]
rs6496878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6496880	0.95[CEU][hapmap]
rs7163871	1.00[CEU][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7174549	0.81[JPT][hapmap]
rs7179958	0.94[ASW][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.82[MKK][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs8027634	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8028382	0.90[JPT][hapmap]
rs8028706	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8032981	1.00[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8037251	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8037463	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048635	chr15:92073294-92557339	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv870094	chr15:92367354-92631647	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv534110	chr15:92397220-92592961	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6496877	AKAP13	cis	parietal	SCAN
rs6496877	NTRK3	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92462800-92482600	Weak transcription	HMEC	breast
2	chr15:92463800-92482400	Weak transcription	Esophagus	oesophagus
3	chr15:92464600-92483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:92466400-92482200	Weak transcription	Pancreas	Pancrea
5	chr15:92466800-92480200	Weak transcription	Fetal Brain Female	brain
6	chr15:92468000-92478800	Weak transcription	Lung	lung
7	chr15:92469400-92483000	Weak transcription	Gastric	stomach
8	chr15:92469400-92485800	Weak transcription	Aorta	Aorta
9	chr15:92470200-92478000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:92470200-92478600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:92470400-92483200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:92470600-92479800	Weak transcription	NHLF	lung
13	chr15:92470800-92478400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr15:92471000-92478400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:92471200-92483600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:92471800-92481400	Weak transcription	Brain Anterior Caudate	brain
17	chr15:92472600-92479200	Weak transcription	Ovary	ovary
18	chr15:92472800-92478600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr15:92472800-92482400	Weak transcription	Spleen	Spleen
20	chr15:92473200-92478400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:92473600-92479800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:92473600-92483200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr15:92474600-92478800	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr15:92474800-92478800	Weak transcription	Right Ventricle	heart
25	chr15:92475000-92478600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:92475200-92479600	Weak transcription	Fetal Brain Male	brain
27	chr15:92475200-92479800	Weak transcription	Brain Angular Gyrus	brain
28	chr15:92475200-92480200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:92475400-92479800	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:92475400-92482600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr15:92475400-92483000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr15:92475400-92483000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:92475400-92484600	Weak transcription	Primary T cells from cord blood	blood
34	chr15:92475800-92482200	Weak transcription	Brain Substantia Nigra	brain
35	chr15:92476200-92479200	Weak transcription	Right Atrium	heart
36	chr15:92477200-92478000	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
37	chr15:92477400-92479800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr15:92477400-92483400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr15:92477600-92478800	Weak transcription	Fetal Heart	heart
40	chr15:92477600-92481800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:92477600-92482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:92477800-92480000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:92477800-92482800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:92477800-92483200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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