Variant report

Variant	rs3121417
Chromosome Location	chr4:3252678-3252679
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3251210..3252923-chr4:3261294..3264079,2	K562	blood:
2	chr4:3251892..3254308-chr4:3255097..3257902,2	MCF-7	breast:
3	chr4:3251580..3254728-chr4:3256046..3259468,3	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs108850	0.90[JPT][hapmap]
rs110501	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs1547410	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16843804	0.82[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs2024115	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2071655	0.81[CHB][hapmap]
rs2071671	0.94[JPT][hapmap]
rs2071703	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2071704	0.80[JPT][hapmap]
rs2157090	0.82[JPT][hapmap]
rs2269499	0.80[JPT][hapmap];0.88[AMR][1000 genomes]
rs2285086	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2530601	0.82[JPT][hapmap]
rs2798221	0.90[JPT][hapmap]
rs3095075	0.96[ASN][1000 genomes]
rs3095077	0.90[JPT][hapmap]
rs3095081	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs3121418	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121419	1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs3129321	0.95[ASN][1000 genomes]
rs3129322	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3135175	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34155847	1.00[ASN][1000 genomes]
rs362268	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs362271	0.80[JPT][hapmap];0.82[AMR][1000 genomes]
rs362272	0.80[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs362273	0.84[JPT][hapmap]
rs362296	1.00[CEU][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs362306	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs362309	0.88[ASN][1000 genomes]
rs362312	0.87[ASN][1000 genomes]
rs362331	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs363064	0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs363066	0.81[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs363096	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs3775061	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3856973	0.86[CHB][hapmap]
rs4690072	0.82[CHB][hapmap]
rs4690073	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs6446727	0.82[JPT][hapmap]
rs6446731	0.81[JPT][hapmap]
rs6844859	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs6855981	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs7659144	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs7661630	0.82[JPT][hapmap]
rs7685686	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs7691627	0.80[JPT][hapmap]
rs82333	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs916171	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs9996868	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv524211	chr4:3215835-3270488	Strong transcription Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv470003	chr4:3215835-3275484	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv878454	chr4:3215835-3305739	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv878457	chr4:3231661-3278517	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv878458	chr4:3235518-3303976	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv878459	chr4:3235518-3310831	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3121417	MSANTD1	cis	Thyroid	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3238000-3259200	Weak transcription	HSMMtube	muscle
3	chr4:3238200-3255200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:3238200-3261400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:3238600-3259800	Weak transcription	NH-A	brain
6	chr4:3241600-3259200	Weak transcription	Small Intestine	intestine
7	chr4:3243000-3260000	Weak transcription	Brain Angular Gyrus	brain
8	chr4:3243400-3254400	Weak transcription	GM12878-XiMat	blood
9	chr4:3243400-3259200	Weak transcription	Colonic Mucosa	Colon
10	chr4:3243400-3259600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:3243600-3258800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr4:3243800-3257400	Weak transcription	Gastric	stomach
13	chr4:3243800-3258000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:3244200-3259400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:3244800-3259600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr4:3245000-3255400	Weak transcription	Esophagus	oesophagus
17	chr4:3245200-3255000	Weak transcription	Pancreas	Pancrea
18	chr4:3245200-3259800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr4:3245200-3260000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr4:3245400-3256600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:3245400-3257800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr4:3245400-3259200	Weak transcription	Ovary	ovary
23	chr4:3245600-3253000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:3245600-3255000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr4:3246000-3255000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:3246200-3258600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr4:3246400-3254000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:3246400-3255000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:3246400-3261000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:3246600-3254800	Weak transcription	Liver	Liver
31	chr4:3246600-3256200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:3246600-3257400	Weak transcription	Right Ventricle	heart
33	chr4:3246600-3257800	Weak transcription	Adipose Nuclei	Adipose
34	chr4:3246600-3261400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:3247000-3255000	Weak transcription	Lung	lung
36	chr4:3247200-3261000	Weak transcription	Aorta	Aorta
37	chr4:3247400-3254800	Weak transcription	Brain Hippocampus Middle	brain
38	chr4:3247600-3268400	Weak transcription	Primary T cells from cord blood	blood
39	chr4:3248200-3259600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr4:3248400-3257400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:3248600-3254600	Weak transcription	Spleen	Spleen
42	chr4:3248600-3255000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:3248800-3260800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:3249600-3260000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr4:3249800-3252800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr4:3250000-3253200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:3250200-3257400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr4:3250600-3255000	Weak transcription	Fetal Muscle Leg	muscle
49	chr4:3251000-3255200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:3251000-3256200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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