Variant report

Variant	rs2475239
Chromosome Location	chr10:116283756-116283757
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116275231..116277888-chr10:116283553..116286227,3	MCF-7	breast:
2	chr10:116260057..116262598-chr10:116283268..116286200,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229668	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10885572	0.83[CHB][hapmap]
rs10885575	0.83[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs11196775	0.85[CEU][hapmap]
rs11196780	0.83[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs11196781	1.00[CHB][hapmap]
rs12569428	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs2145893	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2145894	0.89[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2247528	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2475240	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs2475241	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs2475242	0.89[CHB][hapmap]
rs2483571	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2483585	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2483587	0.83[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2483595	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2483596	0.83[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2497708	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2497710	1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs2497717	0.82[JPT][hapmap]
rs2497718	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2497719	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2497721	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2497722	0.82[CHB][hapmap]
rs6585285	0.81[CEU][hapmap]
rs883768	0.83[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs9421179	0.82[CHB][hapmap];0.81[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	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2475239	PNLIPRP2	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116243000-116286200	Weak transcription	Spleen	Spleen
2	chr10:116276600-116284600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr10:116277000-116283800	Weak transcription	Fetal Stomach	stomach
4	chr10:116277200-116284600	Weak transcription	Brain Angular Gyrus	brain
5	chr10:116277800-116284600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr10:116278200-116284600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr10:116278800-116284600	Enhancers	Primary hematopoietic stem cells	blood
8	chr10:116278800-116284600	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr10:116278800-116285000	Genic enhancers	Left Ventricle	heart
10	chr10:116279400-116283800	Enhancers	Right Ventricle	heart
11	chr10:116279400-116285800	Weak transcription	Psoas Muscle	Psoas
12	chr10:116279800-116284600	Weak transcription	Aorta	Aorta
13	chr10:116279800-116284800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:116279800-116286000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr10:116280000-116286200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr10:116280000-116286200	Weak transcription	Pancreas	Pancrea
17	chr10:116280200-116283800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr10:116280200-116283800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr10:116280200-116284000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:116280200-116284600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr10:116280200-116284600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr10:116280200-116285000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:116280200-116285400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr10:116280200-116285800	Weak transcription	NHLF	lung
25	chr10:116280200-116286200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr10:116280400-116284600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr10:116280400-116284600	Weak transcription	HUVEC	blood vessel
28	chr10:116280400-116285000	Enhancers	A549	lung
29	chr10:116280800-116284400	Weak transcription	HMEC	breast
30	chr10:116280800-116285400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr10:116281000-116284800	Enhancers	Right Atrium	heart
32	chr10:116281200-116284800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr10:116281200-116285000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr10:116281400-116284400	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr10:116281400-116284600	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr10:116281400-116285000	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr10:116281600-116283800	Enhancers	Fetal Muscle Leg	muscle
38	chr10:116281600-116284000	Enhancers	H9 Cell Line	embryonic stem cell
39	chr10:116281600-116284000	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr10:116281600-116284600	Enhancers	H1 Cell Line	embryonic stem cell
41	chr10:116281600-116285200	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr10:116281800-116283800	Weak transcription	Fetal Kidney	kidney
43	chr10:116281800-116284600	Weak transcription	Fetal Intestine Large	intestine
44	chr10:116281800-116286200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr10:116282000-116283800	Weak transcription	NHEK	skin
46	chr10:116282000-116284600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr10:116282000-116285000	Weak transcription	Brain Anterior Caudate	brain
48	chr10:116282000-116286000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr10:116282000-116286000	Weak transcription	Brain Substantia Nigra	brain
50	chr10:116282000-116287000	Active TSS	Ovary	ovary

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