Variant report

Variant	rs2516698
Chromosome Location	chr6:30232374-30232375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30230865..30233061-chr6:30286411..30288696,2	MCF-7	breast:
2	chr6:30230386..30233468-chr6:30310736..30314450,3	MCF-7	breast:
3	chr6:30230361..30234306-chr6:30292594..30296487,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM39-2	chr6:30231053-30234728	NONHSAT108609

Variant related genes	Relation type
ENSG00000241370	Chromatin interaction
ENSG00000231074	Chromatin interaction
ENSG00000270604	Chromatin interaction
ENSG00000204599	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1579220	0.89[EUR][1000 genomes]
rs2508028	0.85[EUR][1000 genomes]
rs2516701	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2516718	0.80[AFR][1000 genomes]
rs6906364	0.89[EUR][1000 genomes]
rs6907399	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6911349	0.89[EUR][1000 genomes]
rs6924952	0.82[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2516698	HCG18	Cis_1M	lymphoblastoid	RTeQTL
rs2516698	LOC401245	cis	multi-tissue	Pritchard

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30228200-30234200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:30228200-30237400	Weak transcription	Aorta	Aorta
3	chr6:30228400-30232400	Weak transcription	Brain Germinal Matrix	brain
4	chr6:30228400-30232400	Weak transcription	Gastric	stomach
5	chr6:30228400-30232800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:30228400-30236800	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:30228400-30238000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:30228400-30238200	Weak transcription	Left Ventricle	heart
9	chr6:30228400-30239600	Weak transcription	HepG2	liver
10	chr6:30228400-30239800	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:30228600-30233000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:30228600-30233200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:30228600-30233200	Weak transcription	Thymus	Thymus
14	chr6:30228600-30233800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:30228600-30234400	Weak transcription	Fetal Brain Female	brain
16	chr6:30228600-30236600	Weak transcription	Brain Substantia Nigra	brain
17	chr6:30228800-30234200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:30228800-30234600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:30228800-30234600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:30229000-30232600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:30229000-30232800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr6:30229000-30232800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:30229000-30234600	Weak transcription	Adipose Nuclei	Adipose
24	chr6:30229000-30234600	Weak transcription	Spleen	Spleen
25	chr6:30229200-30232600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:30229200-30233000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:30229200-30233400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr6:30229200-30235600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:30229400-30234000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:30229400-30234800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:30229400-30235200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:30229400-30236400	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:30229800-30233800	Enhancers	Placenta Amnion	Placenta Amnion
34	chr6:30229800-30234000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:30229800-30234600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr6:30229800-30235000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr6:30230000-30233600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr6:30230400-30232600	Weak transcription	Fetal Stomach	stomach
39	chr6:30230800-30232400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:30230800-30233400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:30230800-30236200	Weak transcription	GM12878-XiMat	blood
42	chr6:30231000-30233200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:30231000-30235000	Strong transcription	Primary B cells from cord blood	blood
44	chr6:30231200-30232600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:30231200-30232600	Enhancers	Hela-S3	cervix
46	chr6:30231400-30232800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:30231400-30233200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:30231400-30233200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr6:30231400-30233200	Enhancers	NHDF-Ad	bronchial
50	chr6:30231400-30233400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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