Variant report

Variant	rs2959930
Chromosome Location	chr15:72598614-72598615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:72597786..72600011-chr15:72766508..72768760,2	K562	blood:
2	chr15:72564850..72566745-chr15:72598121..72600222,2	K562	blood:
3	chr15:72564706..72566745-chr15:72598121..72601390,3	K562	blood:

Variant related genes	Relation type
ENSG00000166233	Chromatin interaction
ENSG00000137817	Chromatin interaction
ENSG00000261423	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1037680	0.80[MEX][hapmap];0.89[TSI][hapmap]
rs11072346	0.80[CHB][hapmap];0.86[TSI][hapmap]
rs12442886	0.84[TSI][hapmap]
rs12591338	0.81[CHB][hapmap]
rs12592044	0.84[MEX][hapmap];0.89[TSI][hapmap]
rs12901886	0.84[MEX][hapmap];0.86[TSI][hapmap]
rs12904652	0.81[TSI][hapmap]
rs16956634	0.82[CHB][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs2856929	0.80[MEX][hapmap];0.89[TSI][hapmap]
rs2912231	0.89[TSI][hapmap]
rs3743224	0.94[TSI][hapmap]
rs4776589	0.82[CHB][hapmap]
rs4777489	0.84[MEX][hapmap];0.81[TSI][hapmap]
rs4777500	0.86[ASN][1000 genomes]
rs7182776	0.89[TSI][hapmap]
rs7183196	0.80[MEX][hapmap];0.84[TSI][hapmap]
rs8192386	0.82[CHB][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap]
rs8192431	0.82[CHB][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap]

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	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
3	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2959930	PKM2	cis	parietal	SCAN
rs2959930	TIPIN	cis	parietal	SCAN
rs2959930	MYO9A	Cis_1M	lymphoblastoid	RTeQTL
rs2959930	SENP8	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72566000-72611400	Weak transcription	Right Ventricle	heart
2	chr15:72567000-72611800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:72573200-72603000	Weak transcription	Fetal Intestine Large	intestine
4	chr15:72578000-72611800	Weak transcription	Ovary	ovary
5	chr15:72579600-72602400	Weak transcription	Primary T cells from cord blood	blood
6	chr15:72582000-72608000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:72582000-72611800	Weak transcription	Spleen	Spleen
8	chr15:72583800-72611600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr15:72590200-72604800	Weak transcription	Aorta	Aorta
10	chr15:72590600-72607600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:72590800-72602000	Weak transcription	Left Ventricle	heart
12	chr15:72595400-72604600	Weak transcription	Lung	lung
13	chr15:72596000-72612400	Weak transcription	Adipose Nuclei	Adipose
14	chr15:72596400-72599000	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:72597000-72600400	Enhancers	Fetal Brain Male	brain
16	chr15:72597200-72598800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr15:72597600-72600400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:72597600-72605800	Weak transcription	Fetal Intestine Small	intestine
19	chr15:72598000-72598800	Flanking Active TSS	Fetal Brain Female	brain
20	chr15:72598000-72600000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:72598000-72600000	Enhancers	Brain Angular Gyrus	brain
22	chr15:72598200-72599000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:72598200-72599800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:72598200-72600000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr15:72598400-72598800	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr15:72598400-72599200	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr15:72598400-72599400	Enhancers	Primary T cells fromperipheralblood	blood
28	chr15:72598600-72599000	Active TSS	Brain Germinal Matrix	brain
29	chr15:72598600-72599200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:72598600-72599200	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr15:72598600-72599200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:72598600-72599200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:72598600-72599200	Active TSS	Brain Anterior Caudate	brain
34	chr15:72598600-72599200	Active TSS	Brain Cingulate Gyrus	brain

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