Variant report

Variant	rs4928171
Chromosome Location	chr3:100106412-100106413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100100916..100102661-chr3:100105714..100108450,2	MCF-7	breast:
2	chr3:100106259..100108062-chr3:100119845..100121872,2	K562	blood:
3	chr3:100104411..100107248-chr3:100108549..100110661,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154174	Chromatin interaction
ENSG00000206535	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1036769	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11711112	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1214374	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12696105	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119686	0.82[AMR][1000 genomes]
rs2289503	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289504	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2316701	0.84[EUR][1000 genomes]
rs277621	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277627	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs277631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277640	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277646	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277648	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277649	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs378535	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs421855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784494	0.97[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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4928171	LNP1	cis	Muscle Skeletal	GTEx
rs4928171	LOC348801	Cis_1M	lymphoblastoid	RTeQTL
rs4928171	LNP1	cis	Thyroid	GTEx
rs4928171	LNP1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100079400-100107600	Strong transcription	Dnd41	blood
2	chr3:100081200-100107000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:100081200-100107000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:100081200-100107800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:100082200-100107200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:100087600-100114600	Weak transcription	Small Intestine	intestine
7	chr3:100089200-100107200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:100090200-100118400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:100091600-100117600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:100096800-100109800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:100096800-100112800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:100099000-100110200	Weak transcription	Spleen	Spleen
13	chr3:100099000-100118600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:100099200-100108600	Weak transcription	Fetal Stomach	stomach
15	chr3:100099800-100117600	Weak transcription	Colonic Mucosa	Colon
16	chr3:100100400-100107200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:100100800-100108000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:100100800-100110800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:100102800-100118200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:100103600-100106800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:100103800-100112800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:100103800-100117600	Weak transcription	Fetal Kidney	kidney
23	chr3:100103800-100118600	Weak transcription	Brain Substantia Nigra	brain
24	chr3:100104000-100107600	Weak transcription	Fetal Brain Female	brain
25	chr3:100104000-100108000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:100104000-100117600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:100104200-100107000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:100104200-100107000	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:100104200-100107000	Weak transcription	K562	blood
30	chr3:100104200-100108000	Weak transcription	Primary T cells from cord blood	blood
31	chr3:100104200-100114600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:100104200-100117600	Weak transcription	Brain Angular Gyrus	brain
33	chr3:100104200-100117600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:100104200-100117600	Weak transcription	Psoas Muscle	Psoas
35	chr3:100104200-100117600	Weak transcription	Thymus	Thymus
36	chr3:100104200-100117800	Weak transcription	Esophagus	oesophagus
37	chr3:100104200-100118200	Weak transcription	HSMMtube	muscle
38	chr3:100104200-100118600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:100104200-100118600	Weak transcription	Aorta	Aorta
40	chr3:100104400-100107400	Enhancers	HepG2	liver
41	chr3:100104400-100107600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:100104400-100110800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr3:100104400-100117200	Weak transcription	NHEK	skin
44	chr3:100104600-100107400	Weak transcription	Brain Germinal Matrix	brain
45	chr3:100104600-100107800	Weak transcription	Brain Hippocampus Middle	brain
46	chr3:100104600-100108600	Weak transcription	Fetal Thymus	thymus
47	chr3:100104600-100109000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:100104600-100117600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:100104600-100117600	Weak transcription	Fetal Brain Male	brain
50	chr3:100104600-100118600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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