Variant report

Variant	rs1020888
Chromosome Location	chr15:57443315-57443316
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	chr15:57438911..57440950-chr15:57443234..57446216,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1430821	1.00[JPT][hapmap]
rs1542508	1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1642932	1.00[ASW][hapmap];1.00[TSI][hapmap]
rs1652736	1.00[JPT][hapmap]
rs16977246	1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs16977269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1841692	1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs2011551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116064	1.00[JPT][hapmap];0.89[YRI][hapmap]
rs213146	1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2566843	1.00[JPT][hapmap]
rs2585084	1.00[JPT][hapmap];0.88[YRI][hapmap]
rs2585110	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap]
rs2585118	1.00[JPT][hapmap];0.84[YRI][hapmap]
rs2593230	1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2593246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2615233	1.00[JPT][hapmap]
rs2615243	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703587	1.00[JPT][hapmap]
rs2703589	1.00[JPT][hapmap]
rs2703620	1.00[JPT][hapmap]
rs2733194	0.91[ASW][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2733195	1.00[JPT][hapmap]
rs2733339	0.91[ASW][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs4494480	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs4774911	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55702628	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56683633	0.80[AFR][1000 genomes]
rs56821483	0.83[AFR][1000 genomes]
rs56901700	0.80[AFR][1000 genomes]
rs58388376	0.86[AFR][1000 genomes]
rs59239112	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59799036	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs604191	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs6493902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493904	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7161894	1.00[JPT][hapmap];0.89[YRI][hapmap]
rs7164557	1.00[JPT][hapmap];0.94[YRI][hapmap]
rs7175983	0.89[YRI][hapmap]
rs7180911	1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs73415456	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025829	1.00[JPT][hapmap];0.89[YRI][hapmap]
rs8037469	0.91[ASW][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs8040557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[EUR][1000 genomes]

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

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57428600-57444000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr15:57433000-57444000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:57438600-57444000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:57439000-57463400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:57439200-57443400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:57439200-57443600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr15:57439200-57443600	Weak transcription	A549	lung
8	chr15:57439200-57443800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr15:57439400-57443600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:57439400-57444000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:57439400-57444000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr15:57439400-57456000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:57439400-57491600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:57439600-57444000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:57440400-57444000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr15:57440600-57443400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr15:57440600-57443400	Enhancers	NHLF	lung
18	chr15:57440800-57450400	Weak transcription	Aorta	Aorta
19	chr15:57441000-57443600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:57441200-57443600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:57441200-57448600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:57441200-57450800	Weak transcription	Esophagus	oesophagus
23	chr15:57441600-57443400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr15:57441600-57443600	Weak transcription	Fetal Lung	lung
25	chr15:57441600-57443600	Weak transcription	Fetal Stomach	stomach
26	chr15:57441600-57443800	Weak transcription	Liver	Liver
27	chr15:57441600-57443800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:57441600-57444200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:57441600-57444600	ZNF genes & repeats	Dnd41	blood
30	chr15:57441600-57445400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:57441600-57447600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr15:57441800-57443400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:57442000-57444000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:57442200-57443600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:57442200-57444000	Strong transcription	Primary T cells from cord blood	blood
36	chr15:57442200-57445000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:57442200-57446800	ZNF genes & repeats	GM12878-XiMat	blood
38	chr15:57442400-57444000	Weak transcription	Right Atrium	heart
39	chr15:57442400-57445600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:57442400-57446600	Weak transcription	Fetal Heart	heart
41	chr15:57442400-57448000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr15:57442400-57450400	Weak transcription	Ovary	ovary
43	chr15:57442600-57443400	Weak transcription	Thymus	Thymus
44	chr15:57442600-57443600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:57442600-57443600	Weak transcription	Primary B cells from cord blood	blood
46	chr15:57442600-57443600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr15:57442600-57443800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:57442600-57444000	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:57442600-57444000	Weak transcription	Fetal Kidney	kidney
50	chr15:57442600-57444000	Weak transcription	Psoas Muscle	Psoas

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