Variant report

Variant	rs938790
Chromosome Location	chr4:48635206-48635207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48635131..48636662-chr4:48655697..48657913,2	K562	blood:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10517225	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11727472	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498166	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505376	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12506770	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508327	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509766	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13110719	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13134960	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565218	0.91[ASN][1000 genomes]
rs16861344	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861347	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1702795	0.96[AMR][1000 genomes]
rs1702800	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1712762	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17609740	1.00[ASN][1000 genomes]
rs17609761	1.00[ASN][1000 genomes]
rs17656189	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656212	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17656255	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814784	0.93[AMR][1000 genomes]
rs1850520	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581223	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945331	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3107023	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235156	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610307	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695388	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695389	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55730515	0.91[ASN][1000 genomes]
rs55884608	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55986500	0.91[ASN][1000 genomes]
rs57893769	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447646	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447648	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825104	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6852840	0.91[ASN][1000 genomes]
rs707719	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73814762	0.91[ASN][1000 genomes]
rs73814763	0.91[ASN][1000 genomes]
rs73814782	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73814798	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817807	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817808	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817809	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817826	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73817827	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690681	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693468	0.91[ASN][1000 genomes]
rs7695730	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695813	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776582	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776586	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776593	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776594	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776596	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776597	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776598	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776599	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48563000-48637400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:48575200-48643000	Weak transcription	HSMMtube	muscle
3	chr4:48578600-48637000	Weak transcription	Esophagus	oesophagus
4	chr4:48588400-48644600	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:48594000-48637400	Weak transcription	Spleen	Spleen
6	chr4:48597800-48644600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr4:48606800-48637800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:48606800-48645000	Weak transcription	Gastric	stomach
9	chr4:48609800-48637000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr4:48614600-48637000	Weak transcription	Small Intestine	intestine
11	chr4:48620200-48637000	Weak transcription	Fetal Lung	lung
12	chr4:48620200-48637400	Weak transcription	Pancreas	Pancrea
13	chr4:48620200-48644800	Weak transcription	Fetal Stomach	stomach
14	chr4:48620600-48635800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:48621200-48637200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr4:48621200-48642400	Weak transcription	Fetal Heart	heart
17	chr4:48621200-48729400	Weak transcription	Thymus	Thymus
18	chr4:48621800-48637400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr4:48621800-48642200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:48621800-48645000	Weak transcription	Lung	lung
21	chr4:48621800-48655800	Weak transcription	Colonic Mucosa	Colon
22	chr4:48622800-48637000	Weak transcription	Adipose Nuclei	Adipose
23	chr4:48622800-48637600	Weak transcription	Liver	Liver
24	chr4:48622800-48644800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr4:48622800-48648400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:48623000-48635600	Weak transcription	NHDF-Ad	bronchial
27	chr4:48623200-48637000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:48623200-48637000	Weak transcription	Psoas Muscle	Psoas
29	chr4:48623200-48637000	Weak transcription	GM12878-XiMat	blood
30	chr4:48623200-48637400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr4:48623200-48637600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:48623200-48638200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:48623400-48635800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:48623400-48637400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr4:48623400-48644400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:48623600-48637000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:48623600-48637000	Weak transcription	HMEC	breast
38	chr4:48623600-48637400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr4:48624400-48637000	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr4:48624600-48635800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr4:48624600-48637000	Weak transcription	NHEK	skin
42	chr4:48625800-48635600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:48625800-48642000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr4:48626600-48638200	Weak transcription	HepG2	liver
45	chr4:48627000-48637000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:48627200-48636800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:48627200-48637000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:48627200-48637000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr4:48627200-48645000	Weak transcription	Fetal Muscle Leg	muscle
50	chr4:48627200-48652400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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