Variant report

Variant	rs2119686
Chromosome Location	chr3:100110360-100110361
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100104411..100107248-chr3:100108549..100110661,2	MCF-7	breast:
2	chr3:100107045..100110476-chr3:100114433..100116956,3	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1036769	0.80[AMR][1000 genomes]
rs11711112	0.82[AMR][1000 genomes]
rs1214374	0.82[AMR][1000 genomes]
rs12696105	0.82[AMR][1000 genomes]
rs2289503	0.80[AMR][1000 genomes]
rs277631	0.82[AMR][1000 genomes]
rs277640	0.82[AMR][1000 genomes]
rs277646	0.82[AMR][1000 genomes]
rs378535	0.81[AMR][1000 genomes]
rs421855	0.82[AMR][1000 genomes]
rs4928171	0.82[AMR][1000 genomes]
rs6781422	0.82[AMR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2119686	LOC348801	Cis_1M	lymphoblastoid	RTeQTL
rs2119686	LNP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100087600-100114600	Weak transcription	Small Intestine	intestine
2	chr3:100090200-100118400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:100091600-100117600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:100096800-100112800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:100099000-100118600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:100099800-100117600	Weak transcription	Colonic Mucosa	Colon
7	chr3:100100800-100110800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:100102800-100118200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:100103800-100112800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:100103800-100117600	Weak transcription	Fetal Kidney	kidney
11	chr3:100103800-100118600	Weak transcription	Brain Substantia Nigra	brain
12	chr3:100104000-100117600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:100104200-100114600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:100104200-100117600	Weak transcription	Brain Angular Gyrus	brain
15	chr3:100104200-100117600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:100104200-100117600	Weak transcription	Psoas Muscle	Psoas
17	chr3:100104200-100117600	Weak transcription	Thymus	Thymus
18	chr3:100104200-100117800	Weak transcription	Esophagus	oesophagus
19	chr3:100104200-100118200	Weak transcription	HSMMtube	muscle
20	chr3:100104200-100118600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:100104200-100118600	Weak transcription	Aorta	Aorta
22	chr3:100104400-100110800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:100104400-100117200	Weak transcription	NHEK	skin
24	chr3:100104600-100117600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:100104600-100117600	Weak transcription	Fetal Brain Male	brain
26	chr3:100104600-100118600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:100104800-100117400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:100105000-100115800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:100105200-100117600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:100105200-100118400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:100105200-100118600	Weak transcription	Placenta	Placenta
32	chr3:100105400-100112600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:100105600-100114600	Weak transcription	Hela-S3	cervix
34	chr3:100105800-100112800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr3:100105800-100114400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:100105800-100118200	Weak transcription	HMEC	breast
37	chr3:100106000-100110800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:100106000-100117600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:100106000-100117800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:100106200-100115400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr3:100106200-100117400	Weak transcription	Osteobl	bone
42	chr3:100106200-100117800	Weak transcription	NH-A	brain
43	chr3:100106200-100118200	Weak transcription	HUVEC	blood vessel
44	chr3:100106400-100115800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr3:100106400-100116800	Weak transcription	Left Ventricle	heart
46	chr3:100106400-100117400	Weak transcription	Fetal Heart	heart
47	chr3:100106400-100117800	Weak transcription	Lung	lung
48	chr3:100106400-100117800	Weak transcription	Ovary	ovary
49	chr3:100106400-100118200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:100106600-100117800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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