Variant report

Variant	rs12905900
Chromosome Location	chr15:57322886-57322887
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	chr15:57316485..57318733-chr15:57320688..57323136,2	K562	blood:
2	chr15:57315197..57318733-chr15:57320688..57324516,3	K562	blood:

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10518894	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10518895	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10518899	0.96[CEU][hapmap]
rs11071305	0.86[EUR][1000 genomes]
rs11071309	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11630195	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11631228	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11631541	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11632069	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11852340	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11853331	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes]
rs11855648	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11858471	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11858783	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12050751	0.96[CEU][hapmap]
rs12898327	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12898844	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12899036	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12899187	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12899915	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12900589	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12900874	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12900986	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12901780	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12903578	0.85[AMR][1000 genomes]
rs12904070	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12904602	0.92[CEU][hapmap]
rs12906042	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12906873	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12906936	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12908670	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12909811	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12910094	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes]
rs12912007	0.80[EUR][1000 genomes]
rs12912210	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12914182	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12914410	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12914425	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12914625	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12915473	0.84[AMR][1000 genomes]
rs12916237	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916958	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12917247	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13313455	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs1430823	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1462156	0.81[CEU][hapmap]
rs1628067	0.80[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17239040	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17819700	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1814585	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1820995	0.89[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2053472	0.90[AMR][1000 genomes]
rs2111891	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2116065	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2116066	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs213149	0.80[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs213164	0.90[AMR][1000 genomes]
rs2169466	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2414490	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2414491	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2414492	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2414494	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2435907	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2439918	0.82[ASN][1000 genomes]
rs2464429	0.89[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2464430	0.89[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2470079	0.85[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2470082	0.84[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2583108	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2585082	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2585087	0.81[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2585088	0.85[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2585102	0.81[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2585112	0.89[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2615231	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs2703576	0.89[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2703577	0.82[ASN][1000 genomes]
rs2703580	0.83[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2733170	0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2733171	0.81[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2733174	0.81[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2733176	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2733177	0.82[ASN][1000 genomes]
rs2733181	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2733188	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs2733332	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs2920264	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2920265	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2920267	0.89[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2920269	0.81[ASN][1000 genomes]
rs2951895	0.81[ASN][1000 genomes]
rs2951899	0.81[JPT][hapmap]
rs2951901	0.85[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2951903	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs2951904	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs2951906	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2957574	0.83[ASN][1000 genomes]
rs2962990	0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2962991	0.89[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2962992	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2962993	0.81[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34262415	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35646942	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3803454	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3803455	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4774250	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs4774898	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4774899	0.90[AMR][1000 genomes]
rs4774902	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4774910	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs4774913	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs62022986	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62022988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62025331	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6493901	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs715338	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7161965	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7170133	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7175436	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs745652	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7496293	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8037901	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs967514	0.89[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12905900	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57307800-57323400	Weak transcription	Pancreas	Pancrea
2	chr15:57308000-57328000	Weak transcription	Gastric	stomach
3	chr15:57308800-57323400	Weak transcription	Small Intestine	intestine
4	chr15:57309200-57323400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:57309400-57323000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr15:57309400-57334600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:57309600-57323200	Weak transcription	Thymus	Thymus
8	chr15:57310800-57323400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:57311000-57347000	Weak transcription	Fetal Intestine Large	intestine
10	chr15:57312400-57323000	Weak transcription	K562	blood
11	chr15:57315600-57328200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:57315600-57328600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr15:57315800-57323000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr15:57316000-57323400	Weak transcription	Primary B cells from cord blood	blood
15	chr15:57316200-57323000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:57316200-57323400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:57316200-57323400	Weak transcription	Fetal Muscle Leg	muscle
18	chr15:57316400-57324000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:57316400-57328200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr15:57316400-57345400	Weak transcription	Fetal Intestine Small	intestine
21	chr15:57316600-57327800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr15:57317600-57326200	Weak transcription	Esophagus	oesophagus
23	chr15:57317800-57323000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:57318200-57323200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr15:57318200-57323400	Weak transcription	Left Ventricle	heart
26	chr15:57318400-57323000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:57318400-57323000	Weak transcription	HepG2	liver
28	chr15:57318400-57323200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:57318400-57323200	Weak transcription	Brain Germinal Matrix	brain
30	chr15:57318400-57323400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:57318400-57323400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr15:57318600-57323000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:57318600-57323000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr15:57318600-57323000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:57318600-57323000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr15:57318600-57323000	Weak transcription	NHDF-Ad	bronchial
37	chr15:57318600-57323200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:57318600-57323200	Weak transcription	HSMM	muscle
39	chr15:57318600-57323200	Weak transcription	Osteobl	bone
40	chr15:57318600-57323400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:57318600-57323400	Weak transcription	Fetal Stomach	stomach
42	chr15:57318600-57323400	Weak transcription	Ovary	ovary
43	chr15:57318600-57323400	Weak transcription	Right Ventricle	heart
44	chr15:57318600-57323400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:57318600-57323800	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr15:57318600-57331000	Weak transcription	Fetal Kidney	kidney
47	chr15:57318600-57335600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:57318800-57323000	Weak transcription	Colon Smooth Muscle	Colon
49	chr15:57318800-57323000	Weak transcription	A549	lung
50	chr15:57318800-57323000	Weak transcription	NHLF	lung

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