Variant report

Variant	rs4285028
Chromosome Location	chr3:121660664-121660665
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10934565	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12488334	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12488851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12489233	0.82[AMR][1000 genomes]
rs12491991	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12493408	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12493952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12496036	0.89[AMR][1000 genomes]
rs12496318	0.92[GIH][hapmap]
rs12497349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12498028	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12629742	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12630486	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12632345	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12637351	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12637968	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12638492	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13067270	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13083557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13089878	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1344279	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1523519	0.95[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes]
rs1920290	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1920291	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1920297	0.85[EUR][1000 genomes]
rs1920298	0.96[GIH][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1920299	0.96[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1920309	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1986368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1986712	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2091664	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2293611	0.89[AMR][1000 genomes]
rs2332033	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2332035	0.82[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs2689285	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2689290	0.92[GIH][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2877560	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2877561	1.00[CHB][hapmap];0.82[CHD][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs28823352	0.84[AMR][1000 genomes]
rs34158925	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34181646	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34478505	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34543553	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34566912	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34696871	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34837785	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35101693	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35415993	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35737776	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35902163	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915060	0.87[EUR][1000 genomes]
rs3942629	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4118376	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4305455	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4676758	0.84[EUR][1000 genomes]
rs6790281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71329246	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71329247	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71329249	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73855465	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73855476	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73855480	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73855481	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7615571	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7623901	0.92[GIH][hapmap]
rs7637495	0.96[GIH][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7640872	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7651226	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[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	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS 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 target site	37 gene(s)	inside rSNPs	diseases
2	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Multiple sclerosis	21833088	GWAS catalog

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4285028	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs4285028	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs4285028	EAF2	cis	cerebellum	SCAN
rs4285028	HEG1	cis	cerebellum	SCAN
rs4285028	IQCB1	cis	Esophagus Muscularis	GTEx
rs4285028	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs4285028	IQCB1	cis	cerebellum	SCAN
rs4285028	EAF2	cis	lymphoblastoid	seeQTL
rs4285028	IQCB1	cis	parietal	SCAN
rs4285028	SLC15A2	cis	parietal	SCAN
rs4285028	SLC15A2	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121615800-121671600	Weak transcription	Pancreas	Pancrea
2	chr3:121625000-121661200	Weak transcription	Thymus	Thymus
3	chr3:121627400-121664600	Weak transcription	Aorta	Aorta
4	chr3:121631800-121664800	Weak transcription	Brain Angular Gyrus	brain
5	chr3:121633200-121661200	Weak transcription	Liver	Liver
6	chr3:121633800-121661200	Weak transcription	Right Ventricle	heart
7	chr3:121634800-121667000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:121635000-121670600	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:121635200-121666800	Weak transcription	Brain Substantia Nigra	brain
10	chr3:121638400-121664800	Weak transcription	Spleen	Spleen
11	chr3:121638600-121661000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:121638800-121661000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:121642400-121661600	Weak transcription	Fetal Thymus	thymus
14	chr3:121644000-121661200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:121646600-121661800	Weak transcription	Ovary	ovary
16	chr3:121646800-121666200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:121650600-121665800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:121650600-121675600	Weak transcription	Brain Anterior Caudate	brain
19	chr3:121651200-121664000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:121656400-121667200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:121656800-121661000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:121656800-121675200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:121657000-121664600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr3:121657200-121662600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:121657400-121661000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:121657600-121661200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr3:121657600-121662600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:121657600-121663200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr3:121657600-121663600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr3:121657600-121666000	Strong transcription	Primary B cells from cord blood	blood
31	chr3:121657800-121665200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr3:121658000-121667000	Strong transcription	Primary hematopoietic stem cells	blood
33	chr3:121659400-121662800	Enhancers	Placenta Amnion	Placenta Amnion
34	chr3:121659600-121661600	Weak transcription	GM12878-XiMat	blood
35	chr3:121659800-121661000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:121659800-121661800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:121660000-121660800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:121660000-121661600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr3:121660000-121661800	Weak transcription	Placenta	Placenta
40	chr3:121660200-121661800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:121660200-121664000	Weak transcription	Primary T cells from cord blood	blood
42	chr3:121660200-121666200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:121660200-121666400	Weak transcription	Lung	lung
44	chr3:121660200-121666800	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:121660200-121670000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:121660200-121671600	Weak transcription	Left Ventricle	heart
47	chr3:121660200-121675200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:121660200-121676600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:121660400-121661200	Enhancers	Fetal Kidney	kidney
50	chr3:121660600-121660800	Enhancers	Small Intestine	intestine

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