Variant report

Variant	rs12900589
Chromosome Location	chr15:57373236-57373237
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57370971..57373246-chr15:57380194..57383118,2	K562	blood:

Extended variants
information (count: 171 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:168)

rs_ID	r²[population]
rs1037956	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1037958	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10518894	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10518895	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10518898	0.95[YRI][hapmap]
rs10518899	0.85[CEU][hapmap]
rs10518904	0.94[YRI][hapmap]
rs11071305	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11071309	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11630195	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs11631541	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11632069	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11635645	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11636100	0.87[ASN][1000 genomes]
rs11637955	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11852340	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11853331	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11855648	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11857507	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11858471	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs11858783	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12050751	0.88[CEU][hapmap]
rs12437713	1.00[YRI][hapmap]
rs12898327	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12898844	0.82[ASN][1000 genomes]
rs12899036	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12899187	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12899904	0.83[ASN][1000 genomes]
rs12899915	0.89[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs12900038	0.84[ASN][1000 genomes]
rs12900874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12900986	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12904602	0.81[CEU][hapmap]
rs12904634	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12904933	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12905900	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12906042	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12906873	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12909402	0.89[ASN][1000 genomes]
rs12910094	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12910170	0.90[ASN][1000 genomes]
rs12912007	0.83[ASN][1000 genomes]
rs12912210	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12912868	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12914182	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12914425	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12915489	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs12916237	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12916958	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12917247	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13313455	0.83[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes]
rs1430823	0.93[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs1462156	0.85[CEU][hapmap]
rs1545728	0.95[JPT][hapmap]
rs1628067	0.91[JPT][hapmap]
rs16953316	0.94[YRI][hapmap]
rs16953323	1.00[YRI][hapmap]
rs16977155	0.94[YRI][hapmap]
rs16977181	0.95[YRI][hapmap]
rs16977199	0.95[YRI][hapmap]
rs16977201	0.95[YRI][hapmap]
rs16977217	0.95[YRI][hapmap]
rs16977218	0.95[YRI][hapmap]
rs16977235	1.00[YRI][hapmap]
rs16977242	1.00[YRI][hapmap]
rs16977244	0.82[YRI][hapmap]
rs16977245	0.95[YRI][hapmap]
rs16977253	1.00[YRI][hapmap]
rs16977272	1.00[YRI][hapmap]
rs16977276	1.00[YRI][hapmap]
rs16977280	1.00[YRI][hapmap]
rs16977284	1.00[YRI][hapmap]
rs16977297	0.95[YRI][hapmap]
rs16977308	0.94[YRI][hapmap]
rs16977312	0.95[YRI][hapmap]
rs16977315	0.95[YRI][hapmap]
rs16977330	0.95[YRI][hapmap]
rs16977333	0.95[YRI][hapmap]
rs16977341	0.95[YRI][hapmap]
rs16977352	0.95[YRI][hapmap]
rs16977353	0.94[YRI][hapmap]
rs16977354	0.87[YRI][hapmap]
rs17239040	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs17239508	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17415738	1.00[YRI][hapmap]
rs17819700	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs1814585	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1820995	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs1867641	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs213149	0.91[JPT][hapmap]
rs2169465	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2169466	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2264904	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2290938	0.84[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs2414490	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs2414491	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2414492	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2435907	0.84[EUR][1000 genomes]
rs2439918	0.84[EUR][1000 genomes]
rs2439919	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2464429	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2464430	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2470079	0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs2470082	0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2585082	0.88[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs2585087	0.95[JPT][hapmap]
rs2585088	0.86[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2585102	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs2585112	0.85[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs2615231	0.82[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes]
rs2703576	0.85[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs2703577	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2703580	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs2733170	0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2733171	0.95[JPT][hapmap]
rs2733174	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs2733177	0.84[EUR][1000 genomes]
rs2733182	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2733185	0.86[EUR][1000 genomes]
rs2733188	0.86[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2733307	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2733332	0.84[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28414972	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28514688	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28648502	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2920264	0.80[EUR][1000 genomes]
rs2920265	0.84[EUR][1000 genomes]
rs2920267	0.86[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2920269	0.87[EUR][1000 genomes]
rs2927189	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2951895	0.81[EUR][1000 genomes]
rs2951898	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2951899	0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2951901	0.86[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2951903	0.85[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs2951904	0.85[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs2951906	0.84[EUR][1000 genomes]
rs2957574	0.83[EUR][1000 genomes]
rs2957591	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2962990	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2962991	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2962992	0.81[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs2962993	0.91[JPT][hapmap]
rs34262415	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs3794613	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs3803454	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs3803455	0.84[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap]
rs41472450	0.94[YRI][hapmap]
rs4238321	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs4353440	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs4774250	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs4774898	0.84[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs4774902	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs4774910	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4774913	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6493901	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs715338	0.85[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap]
rs7161965	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7168387	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7173936	0.86[EUR][1000 genomes]
rs7175436	0.82[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs7183392	0.91[YRI][hapmap]
rs745652	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7496293	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs8037901	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs935326	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs967514	0.82[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes]
rs978274	0.94[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12900589	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
2	chr15:57346000-57374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:57347000-57373400	Weak transcription	Fetal Intestine Small	intestine
4	chr15:57350400-57373400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr15:57350400-57374000	Weak transcription	Ovary	ovary
6	chr15:57353800-57373800	Weak transcription	Left Ventricle	heart
7	chr15:57353800-57406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:57354200-57384600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:57355000-57374000	Weak transcription	Osteobl	bone
10	chr15:57356000-57393400	Weak transcription	Thymus	Thymus
11	chr15:57356400-57373800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:57362800-57384200	Weak transcription	HepG2	liver
13	chr15:57363800-57378200	Weak transcription	Gastric	stomach
14	chr15:57363800-57382000	Weak transcription	Right Atrium	heart
15	chr15:57365200-57374200	Weak transcription	Fetal Kidney	kidney
16	chr15:57365200-57384000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:57365400-57374000	Weak transcription	NHEK	skin
18	chr15:57365600-57385200	Weak transcription	HSMM	muscle
19	chr15:57365800-57374200	Weak transcription	A549	lung
20	chr15:57365800-57384000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:57367000-57374000	Weak transcription	Psoas Muscle	Psoas
22	chr15:57368000-57380400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:57370600-57373600	Enhancers	Primary T cells from cord blood	blood
24	chr15:57371000-57373400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:57371400-57373400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr15:57371600-57375000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr15:57371600-57375200	Enhancers	HUVEC	blood vessel
28	chr15:57371800-57373400	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr15:57371800-57374800	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr15:57371800-57375000	Enhancers	K562	blood
31	chr15:57371800-57382400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr15:57372000-57384000	Weak transcription	Dnd41	blood
33	chr15:57372400-57373400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:57372400-57375200	Enhancers	Fetal Heart	heart
35	chr15:57372600-57373400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr15:57372600-57373800	Enhancers	Brain Hippocampus Middle	brain
37	chr15:57372600-57374000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr15:57372600-57374000	Enhancers	Small Intestine	intestine
39	chr15:57372600-57374200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr15:57372600-57375000	Enhancers	Duodenum Mucosa	Duodenum
41	chr15:57372600-57375000	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr15:57372600-57386000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr15:57372600-57404000	Weak transcription	HSMMtube	muscle
44	chr15:57372600-57404200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr15:57372800-57373400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr15:57372800-57373400	Enhancers	GM12878-XiMat	blood
47	chr15:57372800-57373600	Enhancers	Brain Anterior Caudate	brain
48	chr15:57372800-57374000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr15:57372800-57374200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:57372800-57374200	Weak transcription	Colon Smooth Muscle	Colon

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