Variant report

Variant	rs11259960
Chromosome Location	chr15:83588703-83588704
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83587802..83590481-chr15:83594024..83596342,2	K562	blood:
2	chr15:83586374..83589449-chr15:83652262..83656378,6	MCF-7	breast:
3	chr15:83587874..83590103-chr15:83620550..83623279,3	MCF-7	breast:
4	chr15:83564369..83566248-chr15:83586818..83589163,2	K562	blood:
5	chr15:83586586..83589404-chr15:83610320..83612935,3	MCF-7	breast:
6	chr15:83586563..83590594-chr15:83604214..83607566,4	MCF-7	breast:
7	chr15:83587194..83589625-chr15:83591212..83594715,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103942	Chromatin interaction
ENSG00000259805	Chromatin interaction
ENSG00000169612	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1037403	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs12050725	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12148275	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12441675	1.00[JPT][hapmap]
rs1568657	0.89[JPT][hapmap]
rs2046070	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs2061947	0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2123157	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs2167602	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]
rs4842917	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4842928	0.84[AMR][1000 genomes]
rs4842935	0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.80[MKK][hapmap]
rs4843141	1.00[JPT][hapmap]
rs4843144	0.87[CHB][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs4843145	0.90[ASN][1000 genomes]
rs4843146	0.95[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs6603041	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs8025253	0.81[AMR][1000 genomes]
rs8034220	0.90[ASN][1000 genomes]
rs8043020	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs872598	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs872599	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.95[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11259960	TM6SF1	cis	lymphoblastoid	seeQTL
rs11259960	HOMER2	cis	Nerve Tibial	GTEx
rs11259960	CIB2	cis	cerebellum	SCAN
rs11259960	C15orf26	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83570400-83591600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:83582600-83592600	Enhancers	Liver	Liver
3	chr15:83583200-83597200	Enhancers	Pancreas	Pancrea
4	chr15:83585600-83599200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:83585800-83600000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:83586000-83589400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr15:83586200-83589400	Enhancers	Stomach Mucosa	stomach
8	chr15:83586600-83619400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr15:83586800-83588800	Enhancers	Right Atrium	heart
10	chr15:83587200-83588800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:83587200-83589600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:83587200-83589600	Enhancers	Ovary	ovary
13	chr15:83587400-83589000	Weak transcription	Gastric	stomach
14	chr15:83587600-83590000	Weak transcription	Fetal Muscle Leg	muscle
15	chr15:83587600-83590400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:83587600-83591000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr15:83587600-83591000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr15:83587600-83594000	Weak transcription	Spleen	Spleen
19	chr15:83587800-83589000	Enhancers	Brain Substantia Nigra	brain
20	chr15:83587800-83589400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:83587800-83590000	Weak transcription	Left Ventricle	heart
22	chr15:83587800-83590000	Weak transcription	Right Ventricle	heart
23	chr15:83587800-83590200	Weak transcription	Psoas Muscle	Psoas
24	chr15:83588000-83588800	Enhancers	Colon Smooth Muscle	Colon
25	chr15:83588000-83589400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:83588200-83589000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:83588200-83589000	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr15:83588200-83589200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:83588200-83589200	Weak transcription	Esophagus	oesophagus
30	chr15:83588200-83590400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:83588200-83596600	Weak transcription	Brain Hippocampus Middle	brain
32	chr15:83588400-83589600	Enhancers	HepG2	liver
33	chr15:83588600-83591000	Weak transcription	Brain Angular Gyrus	brain

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