Variant report

Variant	rs12898728
Chromosome Location	chr15:72112853-72112854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10851847	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11633167	0.89[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11634608	0.89[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.90[YRI][hapmap]
rs12050794	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12439494	0.82[CEU][hapmap];0.80[ASN][1000 genomes]
rs12898868	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912771	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1481862	0.81[AMR][1000 genomes]
rs16956273	0.88[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.83[ASN][1000 genomes]
rs16956369	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2128112	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2246225	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs2306576	0.94[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2415120	0.89[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2415121	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2415126	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2415128	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs2625529	0.82[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs2723343	0.82[CEU][hapmap]
rs28650442	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28717020	0.85[AMR][1000 genomes]
rs2929508	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs2929509	0.85[AMR][1000 genomes]
rs2929510	0.87[AMR][1000 genomes]
rs2929511	0.88[AMR][1000 genomes]
rs2930069	0.83[AMR][1000 genomes]
rs2957724	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2957725	0.82[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap]
rs2957728	0.87[AMR][1000 genomes]
rs2957734	0.89[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap]
rs2957735	0.89[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs2957737	0.82[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap]
rs3784309	0.82[CEU][hapmap]
rs3784310	0.89[CEU][hapmap];0.94[MEX][hapmap];0.80[AMR][1000 genomes]
rs3784313	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4511483	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4526973	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4777466	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62023343	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6494973	0.89[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6494975	0.82[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes]
rs7173626	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7175373	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7177242	0.82[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap]
rs7403191	0.81[ASN][1000 genomes]
rs7496582	0.89[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7497104	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8036307	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8040216	0.86[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs8178	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8557	0.94[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8747	0.82[CEU][hapmap]
rs9302260	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs982752	0.82[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.80[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12898728	SENP8	cis	cerebellum	SCAN
rs12898728	TIPIN	cis	parietal	SCAN
rs12898728	PARP6	cis	parietal	SCAN
rs12898728	MYO9A	Cis_1M	lymphoblastoid	RTeQTL
rs12898728	AAGAB	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72100600-72113800	Weak transcription	Fetal Lung	lung
2	chr15:72103400-72114000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:72106000-72114200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr15:72106200-72113800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr15:72106800-72114400	Weak transcription	Fetal Kidney	kidney
6	chr15:72107200-72115200	Weak transcription	Fetal Stomach	stomach
7	chr15:72107800-72115600	Weak transcription	Fetal Heart	heart
8	chr15:72108000-72118600	Weak transcription	Fetal Brain Female	brain
9	chr15:72108600-72120600	Weak transcription	Fetal Brain Male	brain
10	chr15:72110000-72113800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:72110600-72118200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:72110800-72116400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:72110800-72122800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:72111000-72113200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:72111000-72114000	Strong transcription	Fetal Muscle Leg	muscle
16	chr15:72111400-72114000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:72111600-72116600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
18	chr15:72111800-72116400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:72112000-72115800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:72112000-72116200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr15:72112200-72114000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:72112200-72119200	ZNF genes & repeats	A549	lung
23	chr15:72112400-72114000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr15:72112400-72114200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:72112400-72114600	ZNF genes & repeats	HSMMtube	muscle
26	chr15:72112600-72113400	Weak transcription	Left Ventricle	heart
27	chr15:72112600-72114200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:72112600-72114800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:72112800-72113200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
30	chr15:72112800-72114200	Weak transcription	Brain Germinal Matrix	brain
31	chr15:72112800-72118000	ZNF genes & repeats	Liver	Liver

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