Variant report

Variant	rs13858
Chromosome Location	chr15:72433144-72433145
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1000281	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs1035744	0.84[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs10851850	0.84[CEU][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11072349	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072350	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11630170	0.94[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11630611	0.82[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11631650	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11633167	0.81[EUR][1000 genomes]
rs11634608	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11634622	0.82[EUR][1000 genomes]
rs11637611	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11639282	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148078	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12442886	0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs12592044	0.82[TSI][hapmap]
rs12904652	0.90[TSI][hapmap]
rs1481862	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16956369	0.82[EUR][1000 genomes]
rs16956623	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2034879	0.87[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2052713	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2128112	0.83[EUR][1000 genomes]
rs2278987	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2306489	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2415134	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28717020	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2899775	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2899776	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2912231	0.82[TSI][hapmap]
rs2929508	0.86[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2929509	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2929510	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2929511	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2929513	0.88[EUR][1000 genomes]
rs2929517	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2929518	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap]
rs2929525	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2929526	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2929527	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2929532	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2930069	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2957361	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2957365	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2957373	0.89[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs2957724	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2957725	0.89[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs2957728	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2957734	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2957735	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2957736	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2957737	0.89[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs2957740	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2957742	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2957743	0.82[AMR][1000 genomes]
rs2957745	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2957746	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2957750	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35603965	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3759820	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3759900	0.89[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3759902	0.84[AMR][1000 genomes]
rs3784313	0.82[EUR][1000 genomes]
rs4454922	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4506844	0.82[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4777485	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55679065	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55763892	0.82[EUR][1000 genomes]
rs59975112	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62022788	0.82[EUR][1000 genomes]
rs62022789	0.82[EUR][1000 genomes]
rs6494990	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6494992	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6494997	0.84[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs7162299	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7164780	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7170456	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7172158	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7173626	0.82[EUR][1000 genomes]
rs7175197	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7175373	0.89[EUR][1000 genomes]
rs7175792	0.84[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179427	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7179942	0.82[EUR][1000 genomes]
rs7182776	0.82[TSI][hapmap]
rs7183055	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7183196	0.87[TSI][hapmap]
rs7183810	0.82[EUR][1000 genomes]
rs8023788	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025939	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027164	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8027647	0.82[EUR][1000 genomes]
rs8028115	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8030815	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8032222	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8037381	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8038007	0.82[EUR][1000 genomes]
rs8040216	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8040828	0.84[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8182011	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8192362	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8192386	0.80[TSI][hapmap]
rs8192431	0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	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
4	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	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
6	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
rs13858	PARP6	cis	parietal	SCAN
rs13858	AAGAB	cis	cerebellum	SCAN
rs13858	TIPIN	cis	parietal	SCAN
rs13858	SENP8	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72411600-72433800	Weak transcription	Fetal Intestine Small	intestine
2	chr15:72426800-72436200	Weak transcription	Aorta	Aorta
3	chr15:72427400-72433800	Weak transcription	HepG2	liver
4	chr15:72428400-72433800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:72428400-72436000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:72428400-72440400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:72428400-72447400	Weak transcription	Pancreas	Pancrea
8	chr15:72428800-72433200	Weak transcription	Fetal Kidney	kidney
9	chr15:72428800-72433200	Weak transcription	Fetal Stomach	stomach
10	chr15:72428800-72433800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:72428800-72433800	Weak transcription	Small Intestine	intestine
12	chr15:72428800-72433800	Weak transcription	Stomach Mucosa	stomach
13	chr15:72429200-72433800	Weak transcription	A549	lung
14	chr15:72429800-72433800	Weak transcription	Fetal Lung	lung
15	chr15:72429800-72445800	Weak transcription	Fetal Brain Female	brain
16	chr15:72430000-72433800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr15:72430000-72447200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:72430200-72436000	Weak transcription	Fetal Muscle Leg	muscle
19	chr15:72430400-72433800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr15:72430400-72439200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:72430600-72439600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:72430600-72447400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr15:72430800-72435600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:72431000-72433600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:72431000-72433800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:72431000-72433800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:72431000-72433800	Weak transcription	Gastric	stomach
28	chr15:72431200-72433800	Weak transcription	Fetal Intestine Large	intestine
29	chr15:72431200-72433800	Weak transcription	HSMM	muscle
30	chr15:72431400-72447600	Weak transcription	Spleen	Spleen
31	chr15:72431600-72435800	Enhancers	Fetal Heart	heart
32	chr15:72431800-72434400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr15:72432000-72433200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:72432000-72433200	Enhancers	GM12878-XiMat	blood
35	chr15:72432400-72439000	Weak transcription	Brain Anterior Caudate	brain
36	chr15:72432600-72433800	Weak transcription	Left Ventricle	heart
37	chr15:72432600-72434400	Weak transcription	Primary T cells from cord blood	blood
38	chr15:72432600-72437000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr15:72432600-72438200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:72432600-72439200	Weak transcription	Brain Angular Gyrus	brain
41	chr15:72432600-72445600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr15:72432800-72433400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr15:72432800-72433800	Weak transcription	Ovary	ovary
44	chr15:72432800-72433800	Weak transcription	Psoas Muscle	Psoas
45	chr15:72432800-72433800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr15:72432800-72435200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr15:72433000-72439200	Weak transcription	Brain Germinal Matrix	brain

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