Variant report

Variant	rs4577539
Chromosome Location	chr4:88123958-88123959
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr4:88123911-88124384	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:88122608..88124164-chr4:88126529..88128158,2	K562	blood:
2	chr4:87836003..87837844-chr4:88123291..88126235,2	K562	blood:
3	chr4:88122650..88125039-chr4:88136374..88138823,2	K562	blood:

Variant related genes	Relation type
GAPDHP60	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10000784	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10025704	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10029254	1.00[YRI][hapmap]
rs10032710	1.00[ASW][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10034849	1.00[YRI][hapmap]
rs1021104	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10433937	1.00[YRI][hapmap]
rs11946293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13118664	1.00[YRI][hapmap]
rs13130041	1.00[YRI][hapmap]
rs13435265	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1481947	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1552144	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17012516	0.84[AMR][1000 genomes]
rs17012517	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1842685	0.89[MEX][hapmap]
rs28505236	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28571134	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28670747	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28734493	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28882732	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3193672	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3209390	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3733377	0.84[MEX][hapmap]
rs3755980	1.00[ASW][hapmap];0.89[MEX][hapmap]
rs55747890	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs66527077	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72667790	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7437661	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9992651	1.00[YRI][hapmap]

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	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4577539	HSD17B13	cis	parietal	SCAN
rs4577539	HSD17B13	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88081800-88140200	Weak transcription	Aorta	Aorta
2	chr4:88082000-88129200	Weak transcription	Esophagus	oesophagus
3	chr4:88085000-88128000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:88089600-88131000	Weak transcription	Ovary	ovary
5	chr4:88091800-88128000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:88091800-88128600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:88091800-88133600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:88092200-88134800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:88097600-88125200	Weak transcription	Primary B cells from cord blood	blood
10	chr4:88097600-88140400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:88098000-88127400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:88109600-88133600	Weak transcription	Fetal Lung	lung
13	chr4:88110400-88127600	Weak transcription	Liver	Liver
14	chr4:88110800-88128200	Weak transcription	Fetal Intestine Small	intestine
15	chr4:88114600-88129000	Weak transcription	K562	blood
16	chr4:88115400-88128000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr4:88115600-88124400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:88115800-88131000	Weak transcription	Gastric	stomach
19	chr4:88116400-88138000	Weak transcription	HepG2	liver
20	chr4:88117600-88125600	Weak transcription	Fetal Heart	heart
21	chr4:88118800-88127600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr4:88119400-88132600	Weak transcription	Psoas Muscle	Psoas
23	chr4:88121200-88128400	Weak transcription	Right Ventricle	heart
24	chr4:88121200-88130400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr4:88121200-88134600	Weak transcription	Pancreas	Pancrea
26	chr4:88122400-88140000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr4:88123600-88127800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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