Variant report

Variant	rs3775530
Chromosome Location	chr4:75962642-75962643
allele	A/G
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	CUX1	chr4:75962592-75962792	GM12878	blood:	n/a	n/a
2	RUNX3	chr4:75962280-75962888	GM12878	blood:	n/a	n/a
3	EBF1	chr4:75962340-75962977	GM12878	blood:	n/a	chr4:75962733-75962742 chr4:75962731-75962742
4	SPI1	chr4:75962228-75963080	GM12878	blood:	n/a	chr4:75962383-75962392
5	RELA	chr4:75962175-75962876	GM18505	blood:	n/a	chr4:75962291-75962300 chr4:75962291-75962300
6	SPI1	chr4:75962543-75962855	GM12891	blood:	n/a	n/a
7	RELA	chr4:75962136-75962920	GM19099	blood:	n/a	chr4:75962291-75962300 chr4:75962167-75962176 chr4:75962167-75962176 chr4:75962291-75962300
8	RELA	chr4:75962442-75962874	GM19193	blood:	n/a	n/a
9	RELA	chr4:75962465-75962902	GM18951	blood:	n/a	n/a
10	SPI1	chr4:75962564-75962803	GM12878	blood:	n/a	n/a
11	EBF1	chr4:75962528-75962862	GM12878	blood:	n/a	chr4:75962733-75962742 chr4:75962731-75962742
12	SPI1	chr4:75962443-75962853	GM12891	blood:	n/a	n/a
13	SPI1	chr4:75962497-75962824	GM12878	blood:	n/a	n/a
14	MTA3	chr4:75962383-75962904	GM12878	blood:	n/a	n/a
15	EP300	chr4:75962474-75962919	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:75958099..75960578-chr4:75961196..75963622,3	K562	blood:
2	chr4:75960294..75964259-chr4:75966325..75970196,4	K562	blood:

Variant related genes	Relation type
ENSG00000248165	TF binding region
ENSG00000248165	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10007853	0.92[ASN][1000 genomes]
rs10012438	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10015360	0.94[ASN][1000 genomes]
rs10015456	0.89[ASN][1000 genomes]
rs10018358	0.94[ASN][1000 genomes]
rs1043633	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1043634	0.94[ASN][1000 genomes]
rs10518133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11943279	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1346138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16997586	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17000108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17000109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17000112	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17000114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17000141	0.92[ASN][1000 genomes]
rs17000149	0.94[ASN][1000 genomes]
rs17000150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17196260	0.85[CEU][hapmap]
rs17249558	0.85[CEU][hapmap]
rs17250403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17250773	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17386703	0.85[CEU][hapmap]
rs28461358	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28582004	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3733466	0.92[ASN][1000 genomes]
rs3733467	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3796683	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4859933	0.83[ASW][hapmap]
rs6824037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6829853	1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs6836425	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6838268	0.82[CEU][hapmap]
rs6851144	0.91[ASN][1000 genomes]
rs72660383	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72660386	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7654416	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7680016	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7683115	0.94[ASN][1000 genomes]
rs890289	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9090	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[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	nsv1005324	chr4:75689880-76233555	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv537142	chr4:75689880-76233555	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75940000-75976200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:75944200-75971000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:75949800-75963600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr4:75951800-75965200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:75954400-75971000	Weak transcription	Fetal Heart	heart
6	chr4:75956400-75976000	Weak transcription	Spleen	Spleen
7	chr4:75956600-75964800	Weak transcription	Stomach Mucosa	stomach
8	chr4:75956800-75967600	Weak transcription	Colon Smooth Muscle	Colon
9	chr4:75956800-75982800	Weak transcription	Pancreas	Pancrea
10	chr4:75957200-75976400	Weak transcription	Colonic Mucosa	Colon
11	chr4:75957600-75971200	Weak transcription	Fetal Intestine Small	intestine
12	chr4:75959000-75963000	Strong transcription	Aorta	Aorta
13	chr4:75960000-75963000	Enhancers	Primary B cells from peripheral blood	blood
14	chr4:75960600-75963000	Enhancers	GM12878-XiMat	blood
15	chr4:75961000-75963000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr4:75961600-75963200	Enhancers	Adipose Nuclei	Adipose
17	chr4:75961800-75963000	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr4:75962000-75966000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr4:75962200-75962800	Enhancers	Fetal Intestine Large	intestine
20	chr4:75962200-75963000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:75962200-75963000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:75962400-75962800	Enhancers	Fetal Muscle Leg	muscle
23	chr4:75962400-75962800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
24	chr4:75962400-75963000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:75962400-75963000	Enhancers	Psoas Muscle	Psoas
26	chr4:75962400-75963400	Enhancers	Left Ventricle	heart
27	chr4:75962600-75962800	Enhancers	Right Ventricle	heart
28	chr4:75962600-75963200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:75962600-75966000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr4:75962600-75971000	Weak transcription	Right Atrium	heart

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