Variant report

Variant	rs1668590
Chromosome Location	chr15:42253754-42253755
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42253201..42255910-chr15:42263703..42266681,2	K562	blood:
2	chr15:42251806..42254298-chr15:42258394..42260070,2	K562	blood:
3	chr15:42248239..42251142-chr15:42253260..42256152,2	K562	blood:

Variant related genes	Relation type
ENSG00000246740	Chromatin interaction
ENSG00000103966	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1025227	1.00[EUR][1000 genomes]
rs1030417	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1197656	1.00[EUR][1000 genomes]
rs1197676	1.00[EUR][1000 genomes]
rs1197678	1.00[EUR][1000 genomes]
rs1197695	1.00[EUR][1000 genomes]
rs1197696	1.00[EUR][1000 genomes]
rs1197698	1.00[EUR][1000 genomes]
rs1201692	1.00[EUR][1000 genomes]
rs1451047	1.00[ASW][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1530836	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1559882	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1614205	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1621597	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1648808	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1648812	1.00[EUR][1000 genomes]
rs1648819	1.00[EUR][1000 genomes]
rs1648820	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1668566	1.00[EUR][1000 genomes]
rs1668591	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1704402	0.83[LWK][hapmap];1.00[TSI][hapmap]
rs1704408	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1704409	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2665209	1.00[EUR][1000 genomes]
rs2724932	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57032192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73410628	1.00[EUR][1000 genomes]
rs890497	1.00[EUR][1000 genomes]
rs890499	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs890500	1.00[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	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
5	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv1054728	chr15:42177772-42310009	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
8	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42230400-42262200	Weak transcription	Thymus	Thymus
2	chr15:42241200-42259200	Weak transcription	Brain Anterior Caudate	brain
3	chr15:42244200-42259400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr15:42244400-42260600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:42246200-42254600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr15:42246200-42261800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:42246200-42261800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:42246200-42262000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:42246200-42262000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr15:42246400-42258400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:42246400-42259800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:42246400-42262200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:42246600-42258000	Weak transcription	Fetal Stomach	stomach
14	chr15:42246600-42261800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr15:42247800-42258200	Weak transcription	NHLF	lung
16	chr15:42248400-42257600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:42248600-42258200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:42248600-42258200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr15:42248600-42258400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr15:42248600-42263400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr15:42248800-42261800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:42249400-42258200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr15:42249800-42258200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:42250000-42257600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr15:42250000-42258200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr15:42250000-42260000	Weak transcription	Primary T cells from cord blood	blood
27	chr15:42250200-42257600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr15:42250200-42258200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr15:42250200-42258400	Weak transcription	K562	blood
30	chr15:42250200-42260000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:42250200-42261800	Weak transcription	Small Intestine	intestine
32	chr15:42250400-42258200	Weak transcription	Gastric	stomach
33	chr15:42250400-42263600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:42250600-42253800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:42250600-42255400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:42250600-42256000	Weak transcription	Right Ventricle	heart
37	chr15:42250600-42257800	Weak transcription	Primary B cells from cord blood	blood
38	chr15:42250600-42257800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr15:42250600-42258200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr15:42250600-42258200	Weak transcription	Placenta	Placenta
41	chr15:42250600-42258200	Weak transcription	Lung	lung
42	chr15:42250600-42258200	Weak transcription	Right Atrium	heart
43	chr15:42250600-42258400	Weak transcription	Brain Hippocampus Middle	brain
44	chr15:42250600-42259000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:42250600-42259200	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr15:42250600-42259800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr15:42250600-42262800	Weak transcription	Aorta	Aorta
48	chr15:42250800-42257600	Weak transcription	Fetal Muscle Leg	muscle
49	chr15:42250800-42259800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr15:42250800-42261200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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