Variant report

Variant	rs4583911
Chromosome Location	chr5:98367105-98367106
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:98263162..98264704-chr5:98365544..98368385,2	K562	blood:
2	chr5:98362205..98363958-chr5:98366950..98369649,2	MCF-7	breast:
3	chr5:98263067..98265701-chr5:98365532..98368540,4	MCF-7	breast:
4	chr5:98271965..98274046-chr5:98366756..98368349,2	K562	blood:
5	chr5:98265027..98268409-chr5:98365166..98367986,4	K562	blood:
6	chr5:98261108..98266251-chr5:98365242..98369850,9	K562	blood:
7	chr5:98356545..98359049-chr5:98366364..98368367,2	K562	blood:
8	chr5:98263884..98265572-chr5:98366799..98368375,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000153922	Chromatin interaction
ENSG00000248489	Chromatin interaction
ENSG00000200351	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10040066	1.00[CHB][hapmap]
rs10041261	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10050804	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10076291	0.92[ASN][1000 genomes]
rs10477857	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10479345	0.92[ASN][1000 genomes]
rs10479346	0.92[ASN][1000 genomes]
rs10479348	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11242567	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11242574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745405	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11949103	0.92[ASN][1000 genomes]
rs11950452	0.92[ASN][1000 genomes]
rs11950855	0.87[ASN][1000 genomes]
rs11960896	0.92[ASN][1000 genomes]
rs12109067	1.00[ASN][1000 genomes]
rs12189335	0.92[ASN][1000 genomes]
rs12515042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13179812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1393210	1.00[ASN][1000 genomes]
rs1472622	1.00[CHB][hapmap]
rs150935	1.00[YRI][hapmap]
rs151102	1.00[CHB][hapmap]
rs1604450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161729	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs161730	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs161731	1.00[CHB][hapmap]
rs161732	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs161736	1.00[YRI][hapmap]
rs161739	1.00[YRI][hapmap]
rs161746	1.00[YRI][hapmap]
rs161750	1.00[YRI][hapmap]
rs161935	1.00[CHB][hapmap]
rs161936	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs161940	1.00[YRI][hapmap]
rs161943	0.81[AMR][1000 genomes]
rs161947	0.81[AMR][1000 genomes]
rs161957	1.00[YRI][hapmap]
rs167798	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1875529	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2221268	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs246251	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2545735	1.00[YRI][hapmap]
rs2578576	1.00[YRI][hapmap]
rs2578577	1.00[YRI][hapmap]
rs325195	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs325199	1.00[YRI][hapmap]
rs325203	1.00[YRI][hapmap]
rs325204	1.00[YRI][hapmap]
rs325208	1.00[YRI][hapmap]
rs325209	0.82[YRI][hapmap]
rs325220	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs326480	1.00[CHB][hapmap]
rs326481	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs326482	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs327807	1.00[CHB][hapmap]
rs34488	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34489	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs34496	1.00[CHB][hapmap]
rs34498	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs366353	1.00[CHB][hapmap]
rs39660	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs40075	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs4343864	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4448016	1.00[ASN][1000 genomes]
rs4565239	1.00[CHB][hapmap]
rs467728	1.00[CHB][hapmap]
rs4703052	0.92[ASN][1000 genomes]
rs4703340	0.92[ASN][1000 genomes]
rs4703345	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs539024	1.00[CHB][hapmap]
rs6865618	1.00[ASN][1000 genomes]
rs6878136	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6885458	1.00[ASN][1000 genomes]
rs709386	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs709387	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs709388	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs709389	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7449447	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7712408	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7719562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723242	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs819227	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs819230	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs819231	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]

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	nsv1024391	chr5:98355665-98653657	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv599118	chr5:98358191-99029453	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv599119	chr5:98358191-99315677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4583911	RGMB	Cis_1M	lymphoblastoid	RTeQTL
rs4583911	SLCO4C1	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98357400-98368400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr5:98360200-98369000	Enhancers	Primary B cells from peripheral blood	blood
3	chr5:98361200-98368000	Weak transcription	Osteobl	bone
4	chr5:98362000-98367800	Weak transcription	Placenta	Placenta
5	chr5:98362200-98368400	Weak transcription	Small Intestine	intestine
6	chr5:98362400-98368400	Weak transcription	Brain Hippocampus Middle	brain
7	chr5:98362800-98368400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:98363200-98368400	Weak transcription	Fetal Intestine Large	intestine
9	chr5:98363400-98367800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:98363400-98368000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:98363400-98368000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:98363400-98368000	Weak transcription	Fetal Kidney	kidney
13	chr5:98363400-98368000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:98363400-98368200	Weak transcription	Fetal Intestine Small	intestine
15	chr5:98363400-98368200	Weak transcription	Stomach Mucosa	stomach
16	chr5:98363400-98368400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:98363400-98368400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr5:98363600-98367800	Weak transcription	Liver	Liver
19	chr5:98363600-98368000	Weak transcription	Adipose Nuclei	Adipose
20	chr5:98363600-98368000	Weak transcription	A549	lung
21	chr5:98363600-98368400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:98363600-98368400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:98363600-98368600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr5:98364000-98367800	Weak transcription	Dnd41	blood
25	chr5:98364200-98368000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr5:98364200-98368000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:98364200-98368200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr5:98364400-98368200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr5:98364400-98368200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:98364400-98368600	Enhancers	Primary B cells from cord blood	blood
31	chr5:98364600-98368200	Weak transcription	Primary T cells from cord blood	blood
32	chr5:98364800-98367800	Enhancers	GM12878-XiMat	blood
33	chr5:98366000-98367200	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr5:98366200-98367200	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr5:98366200-98368400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:98366200-98368400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr5:98366200-98369400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:98366400-98367200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr5:98366400-98367200	Enhancers	Fetal Thymus	thymus
40	chr5:98366400-98368400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr5:98366400-98368600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr5:98366600-98367200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr5:98366800-98367200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr5:98366800-98368000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr5:98366800-98368000	Weak transcription	Thymus	Thymus
46	chr5:98366800-98368200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr5:98366800-98368200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr5:98366800-98368200	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr5:98366800-98368400	Enhancers	K562	blood
50	chr5:98366800-98368600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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