Variant report

Variant	rs2593217
Chromosome Location	chr15:57506851-57506852
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr15:57505821-57506874	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57506333..57510182-chr15:57512015..57516171,5	K562	blood:

Variant related genes	Relation type
TCF12	TF binding region

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs11071302	0.95[CEU][hapmap]
rs11071307	1.00[CEU][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs11071310	0.95[CEU][hapmap];0.87[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11636655	1.00[CEU][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs12324235	0.95[CEU][hapmap];0.87[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12593843	1.00[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs12595074	0.81[JPT][hapmap]
rs1346880	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs16977329	0.96[YRI][hapmap]
rs17239222	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17239459	0.95[CEU][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs17819940	1.00[CEU][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs17820018	0.95[CEU][hapmap];0.87[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17820095	0.95[CEU][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs1820996	0.95[CEU][hapmap];0.87[JPT][hapmap]
rs1867638	0.95[CEU][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs1867639	0.96[YRI][hapmap]
rs1867641	0.96[YRI][hapmap]
rs1870870	0.95[CEU][hapmap];0.87[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2126402	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2169468	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2248620	1.00[CEU][hapmap];0.87[JPT][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2252289	0.95[CEU][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs2290939	1.00[CEU][hapmap];0.87[JPT][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2431032	0.95[CEU][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs2435905	0.89[CEU][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap]
rs2440972	0.86[EUR][1000 genomes]
rs2440974	0.84[EUR][1000 genomes]
rs2441924	0.82[EUR][1000 genomes]
rs2464427	0.95[CEU][hapmap];0.87[JPT][hapmap]
rs2464428	0.94[CEU][hapmap];0.85[JPT][hapmap]
rs2470080	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs2470081	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs2470083	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs2470084	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs2566856	0.95[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]
rs2591062	1.00[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2591066	1.00[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2593220	0.81[AFR][1000 genomes]
rs2593221	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2593223	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2593233	0.89[EUR][1000 genomes]
rs2593234	0.95[CEU][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs2593236	0.95[CEU][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs2615228	0.89[CEU][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs2703588	0.95[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs2703599	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2703600	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2733187	0.95[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs2733304	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2733309	0.95[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2733316	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs2733317	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs2733318	1.00[CEU][hapmap];0.87[JPT][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2733320	1.00[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs2733323	1.00[YRI][hapmap]
rs2733329	0.85[EUR][1000 genomes]
rs2733330	1.00[CEU][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs2733343	0.93[YRI][hapmap]
rs2733345	0.89[YRI][hapmap]
rs2920270	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2920272	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs2921430	0.95[CEU][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs2951900	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs2951902	0.95[CEU][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes]
rs2957573	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs2957576	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs2957578	0.95[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs2957592	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2962988	0.81[JPT][hapmap]
rs2962994	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs2962995	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3794617	1.00[CEU][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs4378569	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4774920	0.86[EUR][1000 genomes]
rs56151428	0.91[EUR][1000 genomes]
rs6493909	0.95[CEU][hapmap];0.80[JPT][hapmap];0.86[EUR][1000 genomes]
rs7165729	0.91[EUR][1000 genomes]
rs7167268	1.00[CEU][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7180513	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7180558	1.00[YRI][hapmap]
rs7182038	0.95[CEU][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs7182188	1.00[CEU][hapmap];0.87[JPT][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7183392	0.90[CEU][hapmap];0.81[JPT][hapmap]
rs72731924	0.85[EUR][1000 genomes]
rs72731934	0.85[EUR][1000 genomes]
rs72731958	0.89[EUR][1000 genomes]
rs72731964	0.86[EUR][1000 genomes]
rs72731970	0.87[EUR][1000 genomes]
rs72731974	0.91[EUR][1000 genomes]
rs72731986	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs734033	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs8024830	1.00[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs8027348	0.86[EUR][1000 genomes]
rs8035097	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs8037987	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8042190	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs8042322	0.95[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8043103	0.95[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs935328	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs935329	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs997683	1.00[YRI][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	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
2	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
3	nsv457164	chr15:57495060-57559387	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv569578	chr15:57495060-57559387	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57444400-57507400	Weak transcription	K562	blood
2	chr15:57453800-57524600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:57478800-57526200	Weak transcription	Hela-S3	cervix
4	chr15:57479400-57524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:57481800-57524600	Weak transcription	Right Ventricle	heart
6	chr15:57487000-57524400	Weak transcription	Placenta	Placenta
7	chr15:57487200-57511200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr15:57488200-57511600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr15:57491200-57508000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:57491400-57510000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:57491400-57510000	Weak transcription	Psoas Muscle	Psoas
12	chr15:57491400-57510200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr15:57491400-57511200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:57491600-57508000	Weak transcription	HUVEC	blood vessel
15	chr15:57491600-57515200	Weak transcription	GM12878-XiMat	blood
16	chr15:57492400-57511600	Weak transcription	Left Ventricle	heart
17	chr15:57494200-57508600	Weak transcription	Dnd41	blood
18	chr15:57496400-57508000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:57496400-57510200	Weak transcription	Small Intestine	intestine
20	chr15:57501200-57524400	Weak transcription	Thymus	Thymus
21	chr15:57501600-57510200	Weak transcription	Primary B cells from cord blood	blood
22	chr15:57502400-57509600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr15:57503000-57510400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr15:57503400-57508600	Weak transcription	Primary T cells from cord blood	blood
25	chr15:57504000-57507400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:57504200-57508200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:57504400-57507000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr15:57504400-57510200	Enhancers	Brain Hippocampus Middle	brain
29	chr15:57504600-57507000	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr15:57504600-57510000	Enhancers	Brain Anterior Caudate	brain
31	chr15:57504800-57510200	Enhancers	Brain Substantia Nigra	brain
32	chr15:57505000-57507000	Enhancers	Brain Angular Gyrus	brain
33	chr15:57505000-57507200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr15:57505000-57509800	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr15:57505000-57510000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:57505000-57510200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:57505200-57507400	Weak transcription	Fetal Thymus	thymus
38	chr15:57505200-57508000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:57505200-57508000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:57505200-57508200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:57505200-57508200	Enhancers	NHLF	lung
42	chr15:57505200-57510000	Weak transcription	Fetal Muscle Leg	muscle
43	chr15:57505200-57511400	Enhancers	Fetal Lung	lung
44	chr15:57505400-57507400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:57505400-57507600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:57505400-57508400	Enhancers	HSMM	muscle
47	chr15:57505600-57507400	Enhancers	Muscle Satellite Cultured Cells	--
48	chr15:57505600-57507600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:57505800-57507800	Enhancers	HepG2	liver
50	chr15:57505800-57508200	Enhancers	Osteobl	bone

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