Variant report

Variant	rs1299129
Chromosome Location	chr4:79838676-79838677
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79837404..79838979-chr4:79854322..79856124,2	K562	blood:
2	chr4:79510631..79512821-chr4:79838230..79840784,2	K562	blood:
3	chr4:79838465..79840244-chr4:79841781..79843720,2	K562	blood:
4	chr4:79836564..79840244-chr4:79843893..79846943,5	K562	blood:

Extended variants
information (count: 32 )
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];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1061400	0.89[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.85[LWK][hapmap]
rs10857058	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10857059	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]
rs1275046	0.94[CEU][hapmap]
rs1275047	0.94[CEU][hapmap]
rs13108247	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs13122868	0.84[ASW][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap]
rs13123305	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13125525	0.88[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];0.85[LWK][hapmap]
rs1480718	0.88[CEU][hapmap]
rs1871706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1979444	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs2903600	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3937772	0.92[CEU][hapmap]
rs4246709	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4512020	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs6534080	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6534083	0.89[CEU][hapmap]
rs6534090	0.85[MEX][hapmap]
rs6843690	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6854347	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs7657727	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7664339	0.82[GIH][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs7664587	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]
rs7677084	0.95[MEX][hapmap]
rs7690151	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9307446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1299129	PRDM8	cis	parietal	SCAN
rs1299129	LIN54	cis	cerebellum	SCAN
rs1299129	NAAA	cis	parietal	SCAN

Chromatin state (count:115 , 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	chr4:79794200-79850000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:79794200-79859600	Weak transcription	Colonic Mucosa	Colon
4	chr4:79794400-79850000	Weak transcription	Pancreas	Pancrea
5	chr4:79794800-79850200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:79794800-79858000	Weak transcription	HepG2	liver
7	chr4:79796400-79844800	Weak transcription	Fetal Heart	heart
8	chr4:79799200-79858000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:79812000-79842800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr4:79814600-79859600	Weak transcription	Fetal Kidney	kidney
11	chr4:79815200-79845400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr4:79815800-79846600	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:79816000-79848200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:79816200-79848600	Weak transcription	Fetal Lung	lung
15	chr4:79816200-79858400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr4:79816400-79843200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:79827400-79858000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr4:79827400-79858000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr4:79829000-79859200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr4:79829400-79839000	Strong transcription	Dnd41	blood
21	chr4:79830200-79850000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:79830200-79859200	Weak transcription	Hela-S3	cervix
23	chr4:79830600-79839000	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr4:79831000-79850000	Weak transcription	Gastric	stomach
25	chr4:79831200-79858000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr4:79831400-79856600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr4:79833000-79843400	Weak transcription	Brain Germinal Matrix	brain
28	chr4:79833000-79849800	Weak transcription	Fetal Stomach	stomach
29	chr4:79833000-79850000	Weak transcription	Lung	lung
30	chr4:79833000-79850000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr4:79833000-79850000	Weak transcription	Spleen	Spleen
32	chr4:79833000-79850000	Weak transcription	HSMMtube	muscle
33	chr4:79833000-79859800	Weak transcription	Esophagus	oesophagus
34	chr4:79833000-79859800	Weak transcription	Right Ventricle	heart
35	chr4:79833200-79842800	Weak transcription	NHEK	skin
36	chr4:79833200-79843200	Weak transcription	Fetal Muscle Leg	muscle
37	chr4:79833200-79843200	Weak transcription	Osteobl	bone
38	chr4:79833200-79844200	Weak transcription	Fetal Intestine Small	intestine
39	chr4:79833200-79844800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr4:79833200-79845000	Weak transcription	Fetal Brain Female	brain
41	chr4:79833200-79845200	Weak transcription	Left Ventricle	heart
42	chr4:79833200-79845200	Weak transcription	Thymus	Thymus
43	chr4:79833200-79846600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr4:79833200-79847000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:79833200-79847000	Weak transcription	HMEC	breast
46	chr4:79833200-79847400	Weak transcription	Brain Anterior Caudate	brain
47	chr4:79833200-79848600	Weak transcription	Aorta	Aorta
48	chr4:79833200-79848600	Weak transcription	Brain Hippocampus Middle	brain
49	chr4:79833200-79849800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:79833200-79849800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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