Variant report

Variant	rs501679
Chromosome Location	chr4:56237327-56237328
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:56236823..56239564-chr4:56243563..56245351,2	MCF-7	breast:
2	chr4:56235460..56238150-chr4:56260336..56262058,2	MCF-7	breast:
3	chr4:56235502..56237390-chr4:56239912..56242405,3	K562	blood:

Variant related genes	Relation type
ENSG00000249700	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10002541	0.92[CEU][hapmap]
rs10005989	0.91[CEU][hapmap]
rs1011095	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11133376	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11133379	0.92[CEU][hapmap]
rs11133383	0.92[CEU][hapmap];0.81[MEX][hapmap]
rs11133399	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs1128141	0.86[EUR][1000 genomes]
rs11726609	0.92[CEU][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs11735267	0.92[CEU][hapmap]
rs11931061	0.92[CEU][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs11939815	0.92[CEU][hapmap]
rs13102385	0.92[CEU][hapmap]
rs13121235	0.91[CEU][hapmap]
rs13149568	0.81[JPT][hapmap]
rs1522106	0.92[CEU][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs1522111	0.91[CEU][hapmap]
rs2177127	0.92[CEU][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs2177129	0.92[CEU][hapmap]
rs2412643	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2412646	0.92[CEU][hapmap]
rs28665088	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28726308	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3736544	0.92[CEU][hapmap]
rs3805147	0.92[CEU][hapmap]
rs3805154	0.92[CEU][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs3817444	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs4580704	0.92[CEU][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs473005	0.92[CEU][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs480479	0.92[CEU][hapmap]
rs4865010	0.92[CEU][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs6554286	0.96[CEU][hapmap]
rs6811520	0.92[CEU][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs6812042	0.92[CEU][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs6815516	0.92[CEU][hapmap]
rs6819649	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6824955	0.92[CEU][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs6832769	0.92[CEU][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs6837710	0.92[CEU][hapmap]
rs6851838	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs6853192	0.87[CEU][hapmap]
rs726967	0.92[CEU][hapmap]
rs7660054	0.92[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs7667849	0.92[CEU][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs7673908	0.92[CEU][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs7684810	0.87[CEU][hapmap]
rs819271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9312662	0.92[CEU][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs9993675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9997288	0.92[CEU][hapmap];0.90[MEX][hapmap];0.83[TSI][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	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs501679	SRD5A3	cis	parietal	SCAN
rs501679	SRD5A3	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56213600-56242600	Weak transcription	Gastric	stomach
2	chr4:56213800-56239000	Weak transcription	Brain Germinal Matrix	brain
3	chr4:56213800-56251400	Weak transcription	Pancreas	Pancrea
4	chr4:56214000-56237800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr4:56214000-56241800	Weak transcription	Colonic Mucosa	Colon
6	chr4:56214400-56247600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:56219400-56238400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:56220800-56241400	Weak transcription	Primary T cells from cord blood	blood
9	chr4:56225600-56237800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr4:56225800-56237400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:56225800-56238400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:56225800-56244800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:56225800-56244800	Weak transcription	Stomach Mucosa	stomach
14	chr4:56226000-56238400	Weak transcription	Osteobl	bone
15	chr4:56226000-56238600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:56226000-56240400	Weak transcription	HSMM	muscle
17	chr4:56226000-56241200	Weak transcription	Esophagus	oesophagus
18	chr4:56226000-56245000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr4:56226000-56245000	Weak transcription	HSMMtube	muscle
20	chr4:56227800-56238400	Weak transcription	Placenta	Placenta
21	chr4:56228000-56244800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:56228400-56245400	Weak transcription	K562	blood
23	chr4:56228400-56251000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:56230400-56242000	Weak transcription	Ovary	ovary
25	chr4:56230600-56237800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:56230600-56239200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr4:56230600-56239600	Weak transcription	Fetal Brain Female	brain
28	chr4:56230600-56240200	Weak transcription	Fetal Lung	lung
29	chr4:56230600-56241200	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:56230600-56245200	Weak transcription	Fetal Intestine Small	intestine
31	chr4:56231800-56238400	Weak transcription	Thymus	Thymus
32	chr4:56232000-56238200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr4:56232000-56241800	Weak transcription	Lung	lung
34	chr4:56232000-56247600	Weak transcription	Spleen	Spleen
35	chr4:56233200-56238200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr4:56233200-56238400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:56233200-56241800	Weak transcription	Fetal Stomach	stomach
38	chr4:56233200-56261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:56233400-56239400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr4:56233600-56237600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr4:56233600-56237800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr4:56233600-56237800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:56233600-56238000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr4:56233800-56238600	Weak transcription	NH-A	brain
45	chr4:56234000-56244800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:56234200-56237600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:56234200-56238400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr4:56234200-56238600	Weak transcription	Brain Anterior Caudate	brain
49	chr4:56234200-56238600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr4:56234400-56238000	Weak transcription	Brain Inferior Temporal Lobe	brain

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