Variant report

Variant	rs3130405
Chromosome Location	chr6:30234152-30234153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30233853..30235858-chr6:30238091..30240138,2	K562	blood:
2	chr6:30232915..30234566-chr6:30292941..30295302,2	K562	blood:
3	chr17:57919430..57922333-chr6:30232867..30234422,2	MCF-7	breast:
4	chr6:30227118..30230021-chr6:30233412..30236216,2	MCF-7	breast:
5	chr6:30233530..30235918-chr6:30253137..30255680,2	K562	blood:
6	chr6:30230361..30234306-chr6:30292594..30296487,4	MCF-7	breast:
7	chr6:30233837..30236152-chr6:30240056..30242630,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

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

No data

Variant related genes	Relation type
ENSG00000231074	Chromatin interaction
ENSG00000270604	Chromatin interaction
ENSG00000204599	Chromatin interaction
ENSG00000243753	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10484551	0.87[ASN][1000 genomes]
rs16897337	0.87[ASN][1000 genomes]
rs16897339	0.87[ASN][1000 genomes]
rs17194767	0.87[ASN][1000 genomes]
rs2021363	0.87[ASN][1000 genomes]
rs2188100	0.80[EUR][1000 genomes]
rs2285794	0.87[ASN][1000 genomes]
rs2285799	0.87[ASN][1000 genomes]
rs2517612	0.80[EUR][1000 genomes]
rs2523715	0.80[EUR][1000 genomes]
rs2844770	0.93[EUR][1000 genomes]
rs2844771	0.93[EUR][1000 genomes]
rs2844773	0.93[EUR][1000 genomes]
rs2894146	0.87[ASN][1000 genomes]
rs3094070	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3094071	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3094072	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3094073	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3094074	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3094076	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3094077	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3094629	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3094630	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3094632	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129697	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129699	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129700	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129701	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129702	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129703	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3129704	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3129705	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129706	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129707	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129708	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129831	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129832	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129835	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129836	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3129837	0.98[EUR][1000 genomes]
rs3129840	0.98[EUR][1000 genomes]
rs3130398	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130400	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130401	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130403	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130404	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3132650	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3132655	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3132656	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3132657	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3132658	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3132659	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3800332	0.87[ASN][1000 genomes]
rs4711212	0.87[ASN][1000 genomes]
rs4713304	0.87[ASN][1000 genomes]
rs4713306	0.87[ASN][1000 genomes]
rs4713309	0.87[ASN][1000 genomes]
rs4713310	0.82[ASN][1000 genomes]
rs4713311	0.87[ASN][1000 genomes]
rs4713314	0.87[ASN][1000 genomes]
rs56725475	0.87[ASN][1000 genomes]
rs56847466	0.87[ASN][1000 genomes]
rs57715221	0.87[ASN][1000 genomes]
rs58226684	0.87[ASN][1000 genomes]
rs59046803	0.87[ASN][1000 genomes]
rs60925525	0.87[ASN][1000 genomes]
rs61017790	0.87[ASN][1000 genomes]
rs885913	0.80[EUR][1000 genomes]
rs885916	0.82[EUR][1000 genomes]
rs9261629	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9261630	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9261636	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3130405	ZKSCAN3	cis	parietal	SCAN
rs3130405	BTN2A1	cis	parietal	SCAN
rs3130405	BTN3A2	cis	multi-tissue	Pritchard
rs3130405	HLA-A	cis	multi-tissue	Pritchard
rs3130405	ZNF192	cis	cerebellum	SCAN
rs3130405	HLA-H	cis	multi-tissue	Pritchard
rs3130405	HLA-G	cis	multi-tissue	Pritchard
rs3130405	CDSN	cis	multi-tissue	Pritchard
rs3130405	HLA-C	cis	multi-tissue	Pritchard

Chromatin state (count:45 , 50 per page) page: 1

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	chr6:30228400-30236800	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:30228400-30238000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:30228400-30238200	Weak transcription	Left Ventricle	heart
6	chr6:30228400-30239600	Weak transcription	HepG2	liver
7	chr6:30228400-30239800	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:30228600-30234400	Weak transcription	Fetal Brain Female	brain
9	chr6:30228600-30236600	Weak transcription	Brain Substantia Nigra	brain
10	chr6:30228800-30234200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:30228800-30234600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:30228800-30234600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:30229000-30234600	Weak transcription	Adipose Nuclei	Adipose
14	chr6:30229000-30234600	Weak transcription	Spleen	Spleen
15	chr6:30229200-30235600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:30229400-30234800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:30229400-30235200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:30229400-30236400	Weak transcription	Fetal Muscle Leg	muscle
19	chr6:30229800-30234600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:30229800-30235000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr6:30230800-30236200	Weak transcription	GM12878-XiMat	blood
22	chr6:30231000-30235000	Strong transcription	Primary B cells from cord blood	blood
23	chr6:30231600-30239600	Weak transcription	Brain Angular Gyrus	brain
24	chr6:30232000-30234400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:30232200-30234400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr6:30232200-30235200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:30232200-30235800	Weak transcription	Brain Anterior Caudate	brain
28	chr6:30232800-30235600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:30233000-30234400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
30	chr6:30233000-30235200	Weak transcription	Primary T cells from cord blood	blood
31	chr6:30233200-30234800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr6:30233200-30235400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:30233200-30235800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:30233200-30243600	Weak transcription	HSMMtube	muscle
35	chr6:30233400-30235200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:30233400-30235200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:30233400-30235400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:30233400-30235600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:30233400-30236000	Weak transcription	Osteobl	bone
40	chr6:30233600-30235200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr6:30233800-30236200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr6:30233800-30241200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:30234000-30234200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:30234000-30234200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:30234000-30234400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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