Variant report

Variant	rs2525530
Chromosome Location	chr14:69014452-69014453
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68994426..68996258-chr14:69013993..69016421,2	MCF-7	breast:
2	chr14:69013842..69015927-chr14:69025144..69027586,2	MCF-7	breast:
3	chr14:69012961..69014809-chr14:69260230..69262550,2	MCF-7	breast:
4	chr14:69012905..69014587-chr14:69260400..69263200,2	MCF-7	breast:
5	chr14:69013020..69016426-chr14:69030419..69035616,4	MCF-7	breast:
6	chr14:69013185..69015813-chr14:69258202..69261056,2	K562	blood:
7	chr14:69014425..69017204-chr14:69022282..69023965,2	K562	blood:

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10134446	0.92[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1023529	0.93[CHB][hapmap]
rs11158749	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12587232	0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs12887124	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17105828	0.81[LWK][hapmap]
rs2040782	0.86[ASN][1000 genomes]
rs2079211	0.85[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2158358	0.80[ASN][1000 genomes]
rs2189517	0.92[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2244814	0.81[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs2679	0.85[JPT][hapmap];0.80[MEX][hapmap]
rs2842325	0.85[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs2842328	0.86[ASN][1000 genomes]
rs7140266	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs757370	0.83[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs929285	0.85[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs9323513	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.93[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	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv832822	chr14:68874640-69060272	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv516239	chr14:69010690-69025870	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2525530	SIPA1L1	cis	cerebellum	SCAN
rs2525530	HRASLS2	trans	lymphoblastoid	seeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69002400-69016600	Weak transcription	Gastric	stomach
2	chr14:69005000-69015000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:69006000-69014600	Enhancers	NHDF-Ad	bronchial
4	chr14:69006800-69014600	Weak transcription	Brain Angular Gyrus	brain
5	chr14:69009000-69023600	Enhancers	Fetal Muscle Leg	muscle
6	chr14:69009200-69016600	Enhancers	Colon Smooth Muscle	Colon
7	chr14:69009400-69017600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr14:69009600-69014600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr14:69009600-69016000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr14:69010400-69015200	Enhancers	NHLF	lung
11	chr14:69010400-69017000	Enhancers	Pancreas	Pancrea
12	chr14:69010400-69018600	Enhancers	Fetal Stomach	stomach
13	chr14:69010800-69017800	Enhancers	Stomach Mucosa	stomach
14	chr14:69011400-69018000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr14:69012600-69017200	Enhancers	Lung	lung
16	chr14:69012600-69018400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr14:69012800-69015800	Enhancers	Esophagus	oesophagus
18	chr14:69012800-69015800	Enhancers	Psoas Muscle	Psoas
19	chr14:69012800-69019400	Enhancers	Left Ventricle	heart
20	chr14:69012800-69022000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr14:69013000-69015800	Enhancers	Aorta	Aorta
22	chr14:69013000-69019200	Enhancers	Right Atrium	heart
23	chr14:69013200-69016000	Enhancers	Placenta Amnion	Placenta Amnion
24	chr14:69013400-69014600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr14:69013400-69014600	Enhancers	Osteobl	bone
26	chr14:69013400-69014800	Enhancers	Brain Germinal Matrix	brain
27	chr14:69013400-69015000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr14:69013400-69015800	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr14:69013400-69016000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr14:69013400-69016000	Enhancers	Duodenum Mucosa	Duodenum
31	chr14:69013400-69016000	Enhancers	Right Ventricle	heart
32	chr14:69013400-69016000	Flanking Active TSS	NHEK	skin
33	chr14:69013400-69018600	Enhancers	Ovary	ovary
34	chr14:69013400-69022600	Enhancers	HUVEC	blood vessel
35	chr14:69013600-69014600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr14:69013600-69014600	Enhancers	K562	blood
37	chr14:69013600-69015600	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr14:69013600-69016000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr14:69013600-69019000	Enhancers	Fetal Heart	heart
40	chr14:69013600-69019800	Enhancers	Fetal Kidney	kidney
41	chr14:69013600-69021200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr14:69013600-69022600	Enhancers	Adipose Nuclei	Adipose
43	chr14:69013800-69014600	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr14:69013800-69014800	Flanking Active TSS	HSMMtube	muscle
45	chr14:69013800-69015000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr14:69013800-69015000	Flanking Active TSS	Hela-S3	cervix
47	chr14:69013800-69015000	Flanking Active TSS	HSMM	muscle
48	chr14:69013800-69015200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr14:69013800-69015200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr14:69013800-69016000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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