Variant report

Variant	rs2167602
Chromosome Location	chr15:83649292-83649293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83648429..83650845-chr15:83651784..83654033,2	K562	blood:
2	chr15:83648429..83650791-chr15:83651784..83654037,2	K562	blood:
3	chr15:83619910..83621927-chr15:83648101..83650066,2	MCF-7	breast:
4	chr15:83648407..83651273-chr15:83654725..83656444,2	K562	blood:

Variant related genes	Relation type
ENSG00000169612	Chromatin interaction
ENSG00000103942	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1037403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11259960	0.81[CHB][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes]
rs11259963	0.93[ASN][1000 genomes]
rs12050725	0.94[JPT][hapmap];0.82[AMR][1000 genomes]
rs12148275	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs12441675	0.94[JPT][hapmap]
rs1568657	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2046070	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2061947	0.94[JPT][hapmap]
rs2123157	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2123158	0.94[ASN][1000 genomes]
rs2381028	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28451607	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28510273	0.87[ASN][1000 genomes]
rs4842859	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4842917	0.83[AMR][1000 genomes]
rs4842928	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4842935	0.82[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4843141	0.94[JPT][hapmap]
rs4843144	0.85[JPT][hapmap]
rs4843146	0.86[JPT][hapmap]
rs59108707	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6603038	0.96[ASN][1000 genomes]
rs6603041	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8025253	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8034220	0.80[ASN][1000 genomes]
rs8043020	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs872598	0.89[JPT][hapmap]
rs872599	0.81[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2167602	C15orf26	cis	cerebellum	SCAN
rs2167602	TM6SF1	cis	multi-tissue	Pritchard
rs2167602	HOMER2	cis	Nerve Tibial	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83622200-83649400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:83635600-83653800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:83635800-83654000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr15:83640200-83654000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:83640600-83654000	Weak transcription	HSMMtube	muscle
6	chr15:83640800-83654000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr15:83641200-83653800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr15:83641200-83654200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr15:83642000-83653800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr15:83642200-83653800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:83642200-83653800	Weak transcription	HSMM	muscle
12	chr15:83642200-83654000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:83642400-83653800	Weak transcription	Liver	Liver
14	chr15:83644400-83654000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:83644600-83654000	Weak transcription	Primary B cells from cord blood	blood
16	chr15:83644800-83649800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:83644800-83653800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:83644800-83654000	Weak transcription	A549	lung
19	chr15:83645400-83654000	Weak transcription	Brain Anterior Caudate	brain
20	chr15:83645800-83654200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:83646400-83654000	Weak transcription	K562	blood
22	chr15:83647000-83653800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr15:83647400-83653800	Weak transcription	Primary T cells from cord blood	blood
24	chr15:83647600-83654000	Weak transcription	Lung	lung
25	chr15:83647800-83654000	Weak transcription	Thymus	Thymus
26	chr15:83648200-83654000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr15:83649200-83653800	Weak transcription	Brain Substantia Nigra	brain
28	chr15:83649200-83654200	Weak transcription	Placenta	Placenta

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