Variant report

Variant	rs3121418
Chromosome Location	chr4:3251575-3251576
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	chr4:3251210..3252923-chr4:3261294..3264079,2	K562	blood:
2	chr4:3249484..3252398-chr4:3294414..3296079,2	K562	blood:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1547410	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071703	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2269499	0.86[AMR][1000 genomes]
rs3095075	0.96[ASN][1000 genomes]
rs3121417	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121419	0.84[AMR][1000 genomes]
rs3129321	0.95[ASN][1000 genomes]
rs3129322	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3135175	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34155847	1.00[ASN][1000 genomes]
rs362268	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs362271	0.83[AMR][1000 genomes]
rs362272	0.90[AMR][1000 genomes]
rs362296	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs362306	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs362309	0.88[ASN][1000 genomes]
rs362312	0.87[ASN][1000 genomes]
rs3775061	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]

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
rs3121418	MSANTD1	cis	Thyroid	GTEx

Chromatin state (count:77 , 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	chr4:3242200-3252000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr4:3243000-3260000	Weak transcription	Brain Angular Gyrus	brain
9	chr4:3243400-3252000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr4:3243400-3254400	Weak transcription	GM12878-XiMat	blood
11	chr4:3243400-3259200	Weak transcription	Colonic Mucosa	Colon
12	chr4:3243400-3259600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr4:3243600-3258800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr4:3243800-3257400	Weak transcription	Gastric	stomach
15	chr4:3243800-3258000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:3244000-3252200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:3244000-3252200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:3244200-3252400	Weak transcription	Fetal Intestine Large	intestine
19	chr4:3244200-3259400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:3244400-3252000	Weak transcription	Fetal Lung	lung
21	chr4:3244800-3259600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:3245000-3255400	Weak transcription	Esophagus	oesophagus
23	chr4:3245200-3251800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr4:3245200-3255000	Weak transcription	Pancreas	Pancrea
25	chr4:3245200-3259800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr4:3245200-3260000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr4:3245400-3256600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:3245400-3257800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr4:3245400-3259200	Weak transcription	Ovary	ovary
30	chr4:3245600-3252200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr4:3245600-3252200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr4:3245600-3253000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:3245600-3255000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr4:3246000-3255000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:3246200-3251800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:3246200-3258600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr4:3246400-3252000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr4:3246400-3254000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr4:3246400-3255000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:3246400-3261000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:3246600-3254800	Weak transcription	Liver	Liver
42	chr4:3246600-3256200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr4:3246600-3257400	Weak transcription	Right Ventricle	heart
44	chr4:3246600-3257800	Weak transcription	Adipose Nuclei	Adipose
45	chr4:3246600-3261400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:3247000-3252000	Weak transcription	Fetal Intestine Small	intestine
47	chr4:3247000-3255000	Weak transcription	Lung	lung
48	chr4:3247200-3261000	Weak transcription	Aorta	Aorta
49	chr4:3247400-3254800	Weak transcription	Brain Hippocampus Middle	brain
50	chr4:3247600-3268400	Weak transcription	Primary T cells from cord blood	blood

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