Variant report

Variant	rs2625529
Chromosome Location	chr15:72118777-72118778
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1074330	0.85[GIH][hapmap]
rs11072332	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072339	0.90[CHB][hapmap]
rs12898728	0.80[EUR][1000 genomes]
rs12898868	0.80[EUR][1000 genomes]
rs12902006	0.85[GIH][hapmap]
rs12916951	0.82[CHB][hapmap];0.85[GIH][hapmap]
rs16956302	0.86[ASN][1000 genomes]
rs2054601	0.81[CHB][hapmap];0.85[GIH][hapmap]
rs2246225	0.87[CEU][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs2291278	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs2415121	0.80[EUR][1000 genomes]
rs2625530	0.88[ASN][1000 genomes]
rs2723343	0.87[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2723356	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2742323	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs3784309	0.87[CEU][hapmap];0.84[GIH][hapmap]
rs4238447	0.88[ASN][1000 genomes]
rs4776579	0.89[ASN][1000 genomes]
rs4777464	0.89[ASN][1000 genomes]
rs4777466	0.80[EUR][1000 genomes]
rs8178	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs8747	0.87[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs9120	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904334	chr15:71737376-72177659	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1036938	chr15:71948106-72272855	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3331306	chr15:72049818-72427559	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv3433206	chr15:72049838-72427529	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2625529	SENP8	cis	inferior olivary nucleus	BrainEAC
rs2625529	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72108600-72120600	Weak transcription	Fetal Brain Male	brain
2	chr15:72110800-72122800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:72112200-72119200	ZNF genes & repeats	A549	lung
4	chr15:72113000-72118800	Weak transcription	Dnd41	blood
5	chr15:72114200-72118800	Weak transcription	Colonic Mucosa	Colon
6	chr15:72114200-72123200	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr15:72114600-72118800	Weak transcription	Brain Substantia Nigra	brain
8	chr15:72114600-72122600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr15:72114600-72124200	Strong transcription	Placenta	Placenta
10	chr15:72114600-72190600	Weak transcription	Pancreas	Pancrea
11	chr15:72114800-72118800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:72114800-72122600	Strong transcription	Primary T cells from cord blood	blood
13	chr15:72114800-72124600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:72115200-72123000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:72115400-72122800	Strong transcription	HSMM	muscle
16	chr15:72115600-72118800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:72115600-72118800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr15:72115800-72118800	Weak transcription	HUVEC	blood vessel
19	chr15:72115800-72119000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:72115800-72119800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:72115800-72122600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr15:72115800-72122800	Strong transcription	Stomach Smooth Muscle	stomach
23	chr15:72115800-72123200	Strong transcription	Primary B cells from cord blood	blood
24	chr15:72115800-72147000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr15:72116000-72123200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:72116000-72140800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:72116000-72142000	Weak transcription	Hela-S3	cervix
28	chr15:72116200-72122600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:72116200-72122600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr15:72116400-72119200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr15:72116400-72121600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:72116400-72122600	Strong transcription	Left Ventricle	heart
33	chr15:72116400-72122800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:72116400-72147000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr15:72116600-72122400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:72116800-72122600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:72116800-72122600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr15:72116800-72123200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:72117000-72118800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:72117000-72121800	Weak transcription	NHEK	skin
41	chr15:72117000-72122400	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr15:72117000-72122400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr15:72117000-72122800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:72117000-72122800	Strong transcription	Osteobl	bone
45	chr15:72117000-72123000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:72117000-72142800	Weak transcription	Stomach Mucosa	stomach
47	chr15:72117200-72118800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr15:72117200-72122800	Strong transcription	Aorta	Aorta
49	chr15:72117400-72118800	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr15:72117400-72119400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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