Variant report

Variant	rs17819646
Chromosome Location	chr15:57199082-57199083
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57197545..57200478-chr15:57209928..57211970,2	K562	blood:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10518872	1.00[CEU][hapmap]
rs11071298	0.82[EUR][1000 genomes]
rs12437635	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12437714	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12437735	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12437753	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12437777	1.00[AFR][1000 genomes]
rs12438377	0.88[AMR][1000 genomes]
rs12438464	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12438572	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12439010	1.00[AFR][1000 genomes]
rs12439116	1.00[CEU][hapmap]
rs12439149	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12439165	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12439547	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12439697	0.87[AMR][1000 genomes]
rs12439994	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12440245	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12440725	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12440790	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12440891	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12441185	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12441200	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12441263	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12441769	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12441792	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12441888	1.00[AFR][1000 genomes]
rs12441892	1.00[AFR][1000 genomes]
rs12442069	0.88[AMR][1000 genomes]
rs12442238	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12442326	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs12442630	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12442642	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12442662	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12442839	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12443125	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12443178	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1364541	0.82[AMR][1000 genomes]
rs1529597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1631905	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs1647386	0.87[AMR][1000 genomes]
rs1647391	0.84[AMR][1000 genomes]
rs16977123	0.88[AMR][1000 genomes]
rs16977170	1.00[CEU][hapmap]
rs16977201	1.00[CEU][hapmap]
rs17238880	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17238894	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs17238901	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17238950	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17238971	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs17238992	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17239020	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17239047	1.00[AFR][1000 genomes]
rs17239068	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17239089	1.00[AFR][1000 genomes]
rs17239187	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17239208	1.00[AFR][1000 genomes]
rs17239215	1.00[AFR][1000 genomes]
rs17819592	1.00[AFR][1000 genomes]
rs17819616	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs17819658	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17819664	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17819694	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17819755	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17819779	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17819809	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs17819839	1.00[AFR][1000 genomes]
rs17819886	1.00[AFR][1000 genomes]
rs1816322	1.00[AFR][1000 genomes]
rs2161935	1.00[CEU][hapmap]
rs2899599	1.00[CEU][hapmap]
rs4287503	0.82[AMR][1000 genomes]
rs4320591	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs4362334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4424865	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7176472	1.00[CEU][hapmap]
rs966807	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv833020	chr15:57055947-57216068	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv457162	chr15:57083006-57225766	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv569577	chr15:57083006-57225766	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	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
6	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

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57180200-57208000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr15:57181600-57204000	Weak transcription	Thymus	Thymus
3	chr15:57182000-57209200	Weak transcription	Fetal Stomach	stomach
4	chr15:57182600-57204200	Weak transcription	Fetal Thymus	thymus
5	chr15:57191800-57208000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:57194400-57208600	Weak transcription	Left Ventricle	heart
7	chr15:57195400-57199400	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:57195600-57199400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr15:57196000-57205800	Weak transcription	HSMMtube	muscle
10	chr15:57196200-57199200	Weak transcription	Stomach Mucosa	stomach
11	chr15:57196200-57207800	Weak transcription	Fetal Brain Female	brain
12	chr15:57197600-57207200	Weak transcription	Fetal Muscle Leg	muscle
13	chr15:57198000-57199200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:57198800-57199200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:57198800-57199400	Enhancers	HMEC	breast
16	chr15:57198800-57199600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:57199000-57199200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:57199000-57199200	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr15:57199000-57199200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr15:57199000-57199200	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr15:57199000-57199200	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr15:57199000-57199200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr15:57199000-57199200	Active TSS	Duodenum Mucosa	Duodenum
24	chr15:57199000-57199200	Enhancers	GM12878-XiMat	blood
25	chr15:57199000-57199400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:57199000-57199600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:57199000-57199600	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr15:57199000-57199600	Enhancers	Small Intestine	intestine
29	chr15:57199000-57199800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:57199000-57200000	Flanking Active TSS	NHEK	skin
31	chr15:57199000-57200200	Enhancers	Primary B cells from cord blood	blood
32	chr15:57199000-57200400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr15:57199000-57209000	Weak transcription	Brain Germinal Matrix	brain

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