Variant report

Variant	rs10857059
Chromosome Location	chr4:79854436-79854437
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79847059..79848626-chr4:79851803..79854574,2	MCF-7	breast:
2	chr4:79837404..79838979-chr4:79854322..79856124,2	K562	blood:
3	chr4:79846644..79849214-chr4:79851905..79856078,4	K562	blood:

Variant related genes	Relation type
ENSG00000163291	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10028067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061400	0.89[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap]
rs10857058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1275046	0.94[CEU][hapmap]
rs1275047	0.94[CEU][hapmap]
rs1299129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13108247	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs13122868	0.89[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap]
rs13123305	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13125525	0.90[ASN][1000 genomes]
rs13138117	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1426138	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs1480718	0.88[CEU][hapmap]
rs1871706	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979444	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs2903600	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3937772	0.92[CEU][hapmap]
rs4246709	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4512020	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs6534080	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534083	0.89[CEU][hapmap]
rs6534090	0.85[MEX][hapmap]
rs6843690	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6854347	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs7657727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664339	0.82[GIH][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs7664587	1.00[ASW][hapmap];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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677084	0.95[MEX][hapmap];0.85[AMR][1000 genomes]
rs7690151	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][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	nsv879504	chr4:79759796-79874275	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv829979	chr4:79819168-80019159	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1000907	chr4:79838948-80224764	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10857059	NAAA	cis	parietal	SCAN
rs10857059	PRDM8	cis	parietal	SCAN
rs10857059	LIN54	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79779800-79858200	Weak transcription	Fetal Brain Male	brain
2	chr4:79794200-79859600	Weak transcription	Colonic Mucosa	Colon
3	chr4:79794800-79858000	Weak transcription	HepG2	liver
4	chr4:79799200-79858000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:79814600-79859600	Weak transcription	Fetal Kidney	kidney
6	chr4:79816200-79858400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr4:79827400-79858000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:79827400-79858000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr4:79829000-79859200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:79830200-79859200	Weak transcription	Hela-S3	cervix
11	chr4:79831200-79858000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:79831400-79856600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr4:79833000-79859800	Weak transcription	Esophagus	oesophagus
14	chr4:79833000-79859800	Weak transcription	Right Ventricle	heart
15	chr4:79833200-79859000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:79833200-79859600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:79833400-79856800	Weak transcription	GM12878-XiMat	blood
18	chr4:79833600-79858000	Weak transcription	Brain Substantia Nigra	brain
19	chr4:79833600-79859000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:79833600-79859800	Weak transcription	Placenta	Placenta
21	chr4:79835600-79856000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:79836600-79859000	Weak transcription	HSMM	muscle
23	chr4:79840200-79856800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:79841800-79857600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:79842000-79858200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr4:79843800-79855600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:79843800-79858800	Weak transcription	Brain Germinal Matrix	brain
28	chr4:79844200-79855800	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:79844400-79859000	Weak transcription	HUVEC	blood vessel
30	chr4:79844800-79855600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:79845000-79855000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr4:79845200-79859200	Weak transcription	Fetal Heart	heart
33	chr4:79845600-79856200	Weak transcription	Liver	Liver
34	chr4:79845800-79860000	Weak transcription	Small Intestine	intestine
35	chr4:79847400-79858200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:79847600-79858800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr4:79848000-79858000	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:79848000-79859000	Weak transcription	HMEC	breast
39	chr4:79848400-79858800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr4:79848400-79859000	Weak transcription	Brain Angular Gyrus	brain
41	chr4:79849200-79857600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:79849200-79858400	Weak transcription	Psoas Muscle	Psoas
43	chr4:79849200-79859000	Weak transcription	NH-A	brain
44	chr4:79849200-79859600	Weak transcription	Fetal Lung	lung
45	chr4:79850000-79855600	Strong transcription	Dnd41	blood
46	chr4:79850200-79854800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr4:79850400-79858200	Weak transcription	Fetal Intestine Small	intestine
48	chr4:79850400-79859200	Weak transcription	Aorta	Aorta
49	chr4:79850400-79859200	Weak transcription	Fetal Stomach	stomach
50	chr4:79850600-79858000	Weak transcription	Brain Hippocampus Middle	brain

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