Variant report

Variant	rs16880890
Chromosome Location	chr5:52399372-52399373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52398859..52401960-chr5:52403484..52405544,3	K562	blood:
2	chr5:52395948..52400374-chr5:52403348..52406711,5	MCF-7	breast:
3	chr5:52392231..52395065-chr5:52398498..52400912,2	K562	blood:

Variant related genes	Relation type
ENSG00000247796	Chromatin interaction
ENSG00000164172	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10044163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10045657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10051425	0.83[YRI][hapmap]
rs10051483	0.83[YRI][hapmap]
rs10052267	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10064796	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10072821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1042324	0.80[YRI][hapmap]
rs10471372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10471829	0.85[YRI][hapmap]
rs10471830	0.85[YRI][hapmap]
rs10471831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10471832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1445940	0.80[YRI][hapmap]
rs16880872	0.85[YRI][hapmap]
rs16880873	0.80[YRI][hapmap]
rs16880892	0.81[CEU][hapmap]
rs16880902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2052567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2062562	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2233213	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs2233216	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs28841614	0.86[AFR][1000 genomes]
rs28861745	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28890193	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212437	0.86[CHB][hapmap]
rs3212629	0.85[YRI][hapmap]
rs3797468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816326	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs3846488	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4555727	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7446448	0.80[CEU][hapmap]
rs7737412	0.85[YRI][hapmap]
rs875657	0.84[YRI][hapmap]
rs9292008	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9292009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16880890	LAYN	trans	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
3	chr5:52372400-52404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:52378400-52405000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:52387600-52405000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:52389400-52404800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:52390200-52403800	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:52390600-52399600	Strong transcription	NHEK	skin
9	chr5:52390600-52401200	Strong transcription	Dnd41	blood
10	chr5:52390800-52403800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:52391000-52401000	Strong transcription	Duodenum Mucosa	Duodenum
12	chr5:52391000-52403000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:52391600-52403200	Weak transcription	Fetal Heart	heart
14	chr5:52392000-52404800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:52392200-52400800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr5:52392200-52401200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr5:52392400-52400000	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr5:52392400-52400400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr5:52392400-52401400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr5:52392400-52403000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:52392400-52403400	Strong transcription	Liver	Liver
22	chr5:52392400-52404800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr5:52392600-52400400	Strong transcription	Stomach Smooth Muscle	stomach
24	chr5:52392800-52399400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:52392800-52400200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr5:52392800-52400400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:52392800-52401000	Strong transcription	Fetal Muscle Leg	muscle
28	chr5:52392800-52401400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:52392800-52403000	Strong transcription	Adipose Nuclei	Adipose
30	chr5:52392800-52403400	Strong transcription	Left Ventricle	heart
31	chr5:52392800-52403600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:52393000-52405000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr5:52393800-52404800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr5:52394000-52400400	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr5:52394200-52400000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr5:52394200-52400200	Strong transcription	Placenta	Placenta
37	chr5:52394200-52401000	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr5:52394200-52401200	Strong transcription	Primary B cells from peripheral blood	blood
39	chr5:52394600-52399400	Strong transcription	HSMM	muscle
40	chr5:52394600-52400000	Strong transcription	Fetal Intestine Large	intestine
41	chr5:52394600-52402400	Strong transcription	Primary T cells from cord blood	blood
42	chr5:52394600-52402600	Strong transcription	Fetal Thymus	thymus
43	chr5:52394800-52400000	Strong transcription	NHLF	lung
44	chr5:52394800-52403600	Strong transcription	Primary B cells from cord blood	blood
45	chr5:52395400-52402200	Weak transcription	A549	lung
46	chr5:52395400-52404800	Weak transcription	Aorta	Aorta
47	chr5:52395400-52405200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr5:52395600-52403200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr5:52395600-52404400	Weak transcription	Thymus	Thymus
50	chr5:52395600-52404600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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