Variant report

Variant	rs12899485
Chromosome Location	chr15:72143215-72143216
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72137846..72140290-chr15:72140971..72143287,2	K562	blood:

Extended variants
information (count: 121 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10518979	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1074330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11072338	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11072339	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11072346	0.85[EUR][1000 genomes]
rs11633167	0.83[CEU][hapmap]
rs11634608	0.83[CEU][hapmap]
rs11852789	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11853268	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12050895	0.87[EUR][1000 genomes]
rs12439494	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs12439900	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12592364	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12593134	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12593908	0.84[EUR][1000 genomes]
rs12595228	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12595464	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12901580	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12902006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12903484	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12903980	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12906711	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12908300	0.87[EUR][1000 genomes]
rs12911154	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12913042	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914070	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916694	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916951	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12917428	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1384007	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1481861	0.81[EUR][1000 genomes]
rs16956241	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16956273	0.82[CEU][hapmap]
rs16956302	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16956328	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16956381	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16956444	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16956452	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2035379	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2054601	0.84[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2200056	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2246225	0.92[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs2279283	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291278	0.95[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs2306488	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2306490	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2306576	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs2415120	0.83[CEU][hapmap]
rs2415128	0.85[TSI][hapmap]
rs2415130	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2625529	0.85[GIH][hapmap]
rs2625530	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2723342	0.87[CEU][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2723343	0.82[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2723356	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2742323	0.90[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2899773	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2929508	0.84[CEU][hapmap]
rs2929518	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs2957373	0.88[CEU][hapmap]
rs2957724	0.83[CEU][hapmap]
rs2957725	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs2957734	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs2957735	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs2957737	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs34085279	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34137768	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34514871	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35021156	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35115747	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35167572	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35186252	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35258998	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35673773	0.86[EUR][1000 genomes]
rs3784309	0.87[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]
rs4131630	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4238447	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4445848	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4776579	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4776581	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4776584	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4777464	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4777467	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4777469	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4777471	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4777474	0.90[ASN][1000 genomes]
rs4777477	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4777478	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4777480	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4777484	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62023342	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62025574	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6494973	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs6494975	0.88[CEU][hapmap]
rs71395051	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7170461	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7170754	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7172309	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7177242	0.88[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs7183748	0.84[EUR][1000 genomes]
rs7183749	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7403191	0.84[EUR][1000 genomes]
rs7496582	0.83[CEU][hapmap]
rs7497104	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs8025504	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8028115	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs8028532	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8032038	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8747	0.91[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9120	0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs972028	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs972029	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs982752	0.88[CEU][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
5	nsv569906	chr15:72126034-72218036	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv516871	chr15:72126034-72325595	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12899485	TIPIN	cis	parietal	SCAN
rs12899485	SENP8	cis	cerebellum	SCAN
rs12899485	MYO9A	Cis_1M	lymphoblastoid	RTeQTL
rs12899485	PKM2	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72114600-72190600	Weak transcription	Pancreas	Pancrea
2	chr15:72115800-72147000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr15:72116400-72147000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:72119200-72171800	Weak transcription	Psoas Muscle	Psoas
5	chr15:72120600-72147400	Weak transcription	Small Intestine	intestine
6	chr15:72122200-72189400	Weak transcription	Right Ventricle	heart
7	chr15:72122400-72195000	Weak transcription	NHEK	skin
8	chr15:72122600-72144600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:72122600-72145600	Weak transcription	Thymus	Thymus
10	chr15:72122600-72171800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr15:72122600-72185200	Weak transcription	Esophagus	oesophagus
12	chr15:72122600-72195800	Weak transcription	Gastric	stomach
13	chr15:72124800-72145800	Weak transcription	Fetal Heart	heart
14	chr15:72129200-72148000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:72131200-72148200	Strong transcription	Placenta	Placenta
16	chr15:72131600-72147000	Strong transcription	Fetal Muscle Leg	muscle
17	chr15:72131800-72192800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr15:72132000-72145000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr15:72134000-72149000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:72135200-72146600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:72135200-72147600	Strong transcription	Primary T cells from cord blood	blood
22	chr15:72135600-72143800	Strong transcription	Brain Germinal Matrix	brain
23	chr15:72136200-72148400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr15:72136200-72148400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:72136200-72149000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:72136400-72143800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr15:72136400-72145600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr15:72136400-72147000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:72136400-72147000	Strong transcription	Adipose Nuclei	Adipose
30	chr15:72136400-72148400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:72136600-72146600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr15:72136800-72146400	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:72136800-72146400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr15:72136800-72147000	Strong transcription	Primary B cells from cord blood	blood
35	chr15:72137000-72156400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:72137200-72143800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:72137400-72144200	Strong transcription	NHDF-Ad	bronchial
38	chr15:72137600-72143800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr15:72137600-72144400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:72137800-72146000	Strong transcription	Fetal Lung	lung
41	chr15:72137800-72147000	Strong transcription	Stomach Smooth Muscle	stomach
42	chr15:72138200-72144200	Strong transcription	Brain Anterior Caudate	brain
43	chr15:72138200-72146200	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr15:72138200-72172400	Weak transcription	HUVEC	blood vessel
45	chr15:72138400-72143800	Strong transcription	Rectal Smooth Muscle	rectum
46	chr15:72138400-72144600	Strong transcription	Colon Smooth Muscle	Colon
47	chr15:72138400-72145800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:72138400-72146200	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:72138400-72146200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:72138400-72146400	Strong transcription	Skeletal Muscle Male	skeletal muscle

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