Variant report

Variant	rs6704382
Chromosome Location	chr1:169759370-169759371
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169754064..169755659-chr1:169758806..169760332,2	MCF-7	breast:
2	chr1:169757678..169760547-chr22:21995645..21997471,2	K562	blood:
3	chr1:169751112..169752655-chr1:169758575..169760981,2	MCF-7	breast:
4	chr1:169755971..169761352-chr1:169761713..169764832,7	MCF-7	breast:
5	chr1:169758285..169760664-chr1:169861938..169863927,2	K562	blood:

Variant related genes	Relation type
ENSG00000128228	Chromatin interaction
ENSG00000000460	Chromatin interaction
ENSG00000171806	Chromatin interaction
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10753798	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10800478	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2205845	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7529874	0.90[EUR][1000 genomes]
rs9803717	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9803860	0.83[AMR][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	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6704382	SCYL3	Cis_1M	lymphoblastoid	RTeQTL
rs6704382	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169749400-169761400	Weak transcription	Liver	Liver
2	chr1:169750800-169762800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:169751600-169760200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:169751600-169762600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:169752600-169760200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:169753600-169763000	Weak transcription	HMEC	breast
7	chr1:169754400-169760800	Weak transcription	Dnd41	blood
8	chr1:169755000-169760000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:169756400-169761000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:169756400-169762400	Weak transcription	Fetal Brain Male	brain
11	chr1:169756600-169762600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:169757000-169762400	Weak transcription	Fetal Thymus	thymus
13	chr1:169757400-169763000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:169757400-169763000	Weak transcription	Thymus	Thymus
15	chr1:169757400-169763200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:169757600-169762200	Weak transcription	Fetal Intestine Small	intestine
17	chr1:169757600-169763000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr1:169757800-169760000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:169758000-169762800	Weak transcription	Primary B cells from cord blood	blood
20	chr1:169758200-169761200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:169758200-169763200	Weak transcription	Adipose Nuclei	Adipose
22	chr1:169758200-169763200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:169758400-169760000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:169758400-169761600	Weak transcription	HepG2	liver
25	chr1:169758600-169763000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:169758600-169763200	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:169758600-169763200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:169758600-169763400	Weak transcription	Gastric	stomach
29	chr1:169758800-169760000	Weak transcription	Fetal Stomach	stomach
30	chr1:169758800-169762200	Weak transcription	Aorta	Aorta
31	chr1:169758800-169762400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:169758800-169763000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:169758800-169763000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:169758800-169763200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:169758800-169763200	Weak transcription	HSMM	muscle
36	chr1:169758800-169763600	Weak transcription	Spleen	Spleen
37	chr1:169759000-169760600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:169759000-169761000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:169759000-169762600	Weak transcription	Brain Germinal Matrix	brain
40	chr1:169759000-169762800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:169759000-169763000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:169759000-169763000	Weak transcription	A549	lung
43	chr1:169759200-169761000	Weak transcription	Fetal Kidney	kidney
44	chr1:169759200-169761400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:169759200-169763000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:169759200-169763200	Weak transcription	Ovary	ovary
47	chr1:169759200-169763200	Weak transcription	Rectal Mucosa Donor 31	rectum

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