Variant report

Variant	rs1061400
Chromosome Location	chr4:79793707-79793708
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10028067	0.89[CHB][hapmap]
rs10857059	0.89[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap]
rs1299129	0.89[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.85[LWK][hapmap]
rs13122868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13125525	0.93[EUR][1000 genomes]
rs13138117	0.89[CHB][hapmap]
rs1426138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs1871706	0.89[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap]
rs7664587	0.89[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap]
rs9307446	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1061400	LIN54	cis	cerebellum	SCAN
rs1061400	PRDM8	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79744600-79793800	Weak transcription	Psoas Muscle	Psoas
2	chr4:79747200-79815600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:79748800-79823600	Weak transcription	Small Intestine	intestine
4	chr4:79749400-79793800	Weak transcription	Gastric	stomach
5	chr4:79749600-79793800	Weak transcription	Fetal Brain Female	brain
6	chr4:79750400-79797000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:79760600-79794800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:79768400-79811400	Weak transcription	Hela-S3	cervix
9	chr4:79771400-79801000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr4:79779000-79814400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:79779800-79858200	Weak transcription	Fetal Brain Male	brain
12	chr4:79782000-79793800	Weak transcription	Aorta	Aorta
13	chr4:79783200-79801000	Strong transcription	K562	blood
14	chr4:79784000-79793800	Weak transcription	A549	lung
15	chr4:79784000-79811200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:79785000-79793800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:79785000-79832400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:79785200-79793800	Weak transcription	NHEK	skin
19	chr4:79786400-79801000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr4:79786600-79800600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:79786600-79801000	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr4:79786600-79831800	Weak transcription	Spleen	Spleen
23	chr4:79786800-79801000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:79787000-79795400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:79787400-79793800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:79787400-79811400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr4:79787600-79793800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr4:79787800-79802200	Strong transcription	Fetal Intestine Large	intestine
29	chr4:79788400-79793800	Weak transcription	Lung	lung
30	chr4:79789600-79793800	Weak transcription	Brain Substantia Nigra	brain
31	chr4:79790200-79793800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:79790200-79810400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr4:79791000-79800800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:79791000-79802400	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr4:79791200-79800800	Strong transcription	HSMM	muscle
36	chr4:79791400-79795200	Strong transcription	Colon Smooth Muscle	Colon
37	chr4:79791400-79795400	Strong transcription	Dnd41	blood
38	chr4:79791400-79797000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:79791400-79801000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:79791400-79801000	Strong transcription	Liver	Liver
41	chr4:79791600-79794800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:79791600-79795000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr4:79791600-79796400	Strong transcription	NHLF	lung
44	chr4:79791600-79801000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr4:79791600-79801200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:79791800-79795000	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr4:79791800-79795000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:79791800-79795400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:79791800-79795400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr4:79791800-79795400	Strong transcription	Left Ventricle	heart

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