Variant report

Variant	rs3129701
Chromosome Location	chr6:30232672-30232673
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
ENSG00000204599	Chromatin interaction
ENSG00000270604	Chromatin interaction
ENSG00000231074	Chromatin interaction
ENSG00000241370	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10484551	1.00[ASN][1000 genomes]
rs16897337	1.00[ASN][1000 genomes]
rs16897339	1.00[ASN][1000 genomes]
rs17188212	0.83[ASN][1000 genomes]
rs17194565	0.83[ASN][1000 genomes]
rs17194767	1.00[ASN][1000 genomes]
rs2021363	1.00[ASN][1000 genomes]
rs2021364	0.91[ASN][1000 genomes]
rs2188100	0.80[EUR][1000 genomes]
rs2285794	1.00[ASN][1000 genomes]
rs2285799	1.00[ASN][1000 genomes]
rs2517612	0.80[EUR][1000 genomes]
rs2523715	0.80[EUR][1000 genomes]
rs2844770	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2844771	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2844773	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2894146	1.00[ASN][1000 genomes]
rs3094070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094076	0.98[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3094077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094629	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3094630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3129704	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3129705	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129706	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129708	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129835	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129836	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3129837	0.98[EUR][1000 genomes]
rs3129840	0.98[EUR][1000 genomes]
rs3130398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130405	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3132650	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3132655	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778625	0.91[ASN][1000 genomes]
rs3800332	1.00[ASN][1000 genomes]
rs4711210	0.83[ASN][1000 genomes]
rs4711212	1.00[ASN][1000 genomes]
rs4713302	0.83[ASN][1000 genomes]
rs4713304	1.00[ASN][1000 genomes]
rs4713306	1.00[ASN][1000 genomes]
rs4713309	1.00[ASN][1000 genomes]
rs4713310	0.95[ASN][1000 genomes]
rs4713311	1.00[ASN][1000 genomes]
rs4713312	0.91[ASN][1000 genomes]
rs4713313	0.91[ASN][1000 genomes]
rs4713314	1.00[ASN][1000 genomes]
rs56707099	0.91[ASN][1000 genomes]
rs56725475	1.00[ASN][1000 genomes]
rs56812420	0.86[ASN][1000 genomes]
rs56847466	1.00[ASN][1000 genomes]
rs57686281	0.83[ASN][1000 genomes]
rs57708012	0.89[ASN][1000 genomes]
rs57715221	1.00[ASN][1000 genomes]
rs58226684	1.00[ASN][1000 genomes]
rs59046803	1.00[ASN][1000 genomes]
rs60925525	1.00[ASN][1000 genomes]
rs61017790	1.00[ASN][1000 genomes]
rs61619108	0.91[ASN][1000 genomes]
rs885913	0.80[EUR][1000 genomes]
rs885916	0.82[EUR][1000 genomes]
rs9261629	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261630	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3129701	ZKSCAN3	cis	parietal	SCAN
rs3129701	ZNF192	cis	cerebellum	SCAN
rs3129701	HLA-C	Cis_chr	lymphoblastoid	RTeQTL
rs3129701	BTN2A1	cis	parietal	SCAN

Chromatin state (count:61 , 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	chr6:30228400-30232800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:30228400-30236800	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:30228400-30238000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:30228400-30238200	Weak transcription	Left Ventricle	heart
7	chr6:30228400-30239600	Weak transcription	HepG2	liver
8	chr6:30228400-30239800	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:30228600-30233000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:30228600-30233200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:30228600-30233200	Weak transcription	Thymus	Thymus
12	chr6:30228600-30233800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr6:30228600-30234400	Weak transcription	Fetal Brain Female	brain
14	chr6:30228600-30236600	Weak transcription	Brain Substantia Nigra	brain
15	chr6:30228800-30234200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:30228800-30234600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:30228800-30234600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:30229000-30232800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr6:30229000-30232800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:30229000-30234600	Weak transcription	Adipose Nuclei	Adipose
21	chr6:30229000-30234600	Weak transcription	Spleen	Spleen
22	chr6:30229200-30233000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:30229200-30233400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:30229200-30235600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:30229400-30234000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:30229400-30234800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:30229400-30235200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:30229400-30236400	Weak transcription	Fetal Muscle Leg	muscle
29	chr6:30229800-30233800	Enhancers	Placenta Amnion	Placenta Amnion
30	chr6:30229800-30234000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:30229800-30234600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr6:30229800-30235000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:30230000-30233600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr6:30230800-30233400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:30230800-30236200	Weak transcription	GM12878-XiMat	blood
36	chr6:30231000-30233200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:30231000-30235000	Strong transcription	Primary B cells from cord blood	blood
38	chr6:30231400-30232800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:30231400-30233200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:30231400-30233200	Enhancers	Muscle Satellite Cultured Cells	--
41	chr6:30231400-30233200	Enhancers	NHDF-Ad	bronchial
42	chr6:30231400-30233400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:30231400-30233400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:30231600-30233000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr6:30231600-30233000	Enhancers	Osteobl	bone
46	chr6:30231600-30233200	Enhancers	NHLF	lung
47	chr6:30231600-30239600	Weak transcription	Brain Angular Gyrus	brain
48	chr6:30231800-30232800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr6:30231800-30233400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:30232000-30233200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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