Variant report

Variant	rs378535
Chromosome Location	chr3:100076688-100076689
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100052816..100055133-chr3:100074456..100078103,3	MCF-7	breast:
2	chr3:100055925..100057917-chr3:100076174..100079116,2	MCF-7	breast:
3	chr3:100076004..100077691-chr3:100081043..100083943,2	K562	blood:
4	chr3:100075933..100077541-chr3:100081151..100083943,3	K562	blood:

Variant related genes	Relation type
ENSG00000114021	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	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11711112	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1214374	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12696105	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2119686	0.81[AMR][1000 genomes]
rs2289503	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2289504	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2316701	0.81[EUR][1000 genomes]
rs277621	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs277627	0.90[EUR][1000 genomes]
rs277631	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs277640	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs277646	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs277648	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs277649	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs421855	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4928171	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6781422	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6784494	0.81[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
rs378535	LOC348801	Cis_1M	lymphoblastoid	RTeQTL
rs378535	LNP1	cis	Esophagus Muscularis	GTEx
rs378535	LNP1	cis	Muscle Skeletal	GTEx
rs378535	NIT2	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100054200-100081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:100054800-100081000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:100054800-100097200	Weak transcription	Stomach Mucosa	stomach
5	chr3:100054800-100102200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:100055000-100082400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:100069400-100082400	Weak transcription	Fetal Brain Male	brain
8	chr3:100069600-100080600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:100069600-100083800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:100069600-100085800	Weak transcription	Small Intestine	intestine
11	chr3:100069600-100087000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:100071000-100077600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:100071000-100080800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:100071000-100087800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:100071000-100087800	Strong transcription	Fetal Muscle Trunk	muscle
16	chr3:100071000-100093600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:100071000-100103200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:100071000-100104400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:100071200-100076800	Strong transcription	Primary hematopoietic stem cells	blood
20	chr3:100071200-100077000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:100071200-100077200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:100071200-100077600	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:100071200-100077800	Strong transcription	Adipose Nuclei	Adipose
24	chr3:100071200-100077800	Strong transcription	Dnd41	blood
25	chr3:100071200-100078600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:100071200-100080800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:100071200-100081000	Strong transcription	A549	lung
28	chr3:100071400-100077400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr3:100071400-100082200	Strong transcription	NHEK	skin
30	chr3:100071400-100088000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:100071400-100105800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:100071600-100079600	Weak transcription	Fetal Kidney	kidney
33	chr3:100071600-100080800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:100071600-100087000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:100071800-100084200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:100071800-100090600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:100072000-100084200	Weak transcription	K562	blood
38	chr3:100072200-100080600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:100072200-100081000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:100072200-100081000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:100072400-100077000	Weak transcription	HepG2	liver
42	chr3:100072400-100080200	Weak transcription	HUVEC	blood vessel
43	chr3:100072400-100080800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:100072600-100084800	Weak transcription	Hela-S3	cervix
45	chr3:100072800-100079400	Weak transcription	Osteobl	bone
46	chr3:100073200-100079600	Weak transcription	Fetal Lung	lung
47	chr3:100073200-100080800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:100073200-100082400	Weak transcription	NHLF	lung
49	chr3:100073200-100090200	Weak transcription	Esophagus	oesophagus
50	chr3:100073400-100090400	Weak transcription	Pancreas	Pancrea

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