Variant report

Variant	rs3129704
Chromosome Location	chr6:30234700-30234701
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30233853..30235858-chr6:30238091..30240138,2	K562	blood:
2	chr6:30227118..30230021-chr6:30233412..30236216,2	MCF-7	breast:
3	chr6:30233530..30235918-chr6:30253137..30255680,2	K562	blood:
4	chr6:30233837..30236152-chr6:30240056..30242630,2	MCF-7	breast:

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

Variant related genes	Relation type
ENSG00000243753	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs17188470	1.00[ASN][1000 genomes]
rs17194789	1.00[ASN][1000 genomes]
rs17194852	1.00[ASN][1000 genomes]
rs17194859	1.00[ASN][1000 genomes]
rs2844770	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844771	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844773	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094070	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3094071	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3094072	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3094073	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3094074	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3094076	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094077	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3094629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094630	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3094632	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3129697	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3129699	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3129700	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3129701	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3129702	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3129703	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3129705	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3129706	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3129707	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3129708	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3129831	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3129832	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3129835	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3129836	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129837	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129840	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130398	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3130400	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3130401	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3130403	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3130404	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3130405	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3132650	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132655	0.96[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3132656	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3132657	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3132658	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3132659	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs885916	0.81[EUR][1000 genomes]
rs9261629	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9261630	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9261636	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv884061	chr6:30234627-30250450	Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3129704	ZKSCAN3	cis	parietal	SCAN
rs3129704	ZNF192	cis	cerebellum	SCAN
rs3129704	BTN2A1	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30228200-30237400	Weak transcription	Aorta	Aorta
2	chr6:30228400-30236800	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:30228400-30238000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:30228400-30238200	Weak transcription	Left Ventricle	heart
5	chr6:30228400-30239600	Weak transcription	HepG2	liver
6	chr6:30228400-30239800	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:30228600-30236600	Weak transcription	Brain Substantia Nigra	brain
8	chr6:30229200-30235600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:30229400-30234800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:30229400-30235200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:30229400-30236400	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:30229800-30235000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:30230800-30236200	Weak transcription	GM12878-XiMat	blood
14	chr6:30231000-30235000	Strong transcription	Primary B cells from cord blood	blood
15	chr6:30231600-30239600	Weak transcription	Brain Angular Gyrus	brain
16	chr6:30232200-30235200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:30232200-30235800	Weak transcription	Brain Anterior Caudate	brain
18	chr6:30232800-30235600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:30233000-30235200	Weak transcription	Primary T cells from cord blood	blood
20	chr6:30233200-30234800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:30233200-30235400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:30233200-30235800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:30233200-30243600	Weak transcription	HSMMtube	muscle
24	chr6:30233400-30235200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:30233400-30235200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:30233400-30235400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:30233400-30235600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:30233400-30236000	Weak transcription	Osteobl	bone
29	chr6:30233600-30235200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr6:30233800-30236200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr6:30233800-30241200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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