Variant report

Variant	rs853682
Chromosome Location	chr6:28295875-28295876
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28293963..28296628-chr6:28301528..28305497,4	MCF-7	breast:
2	chr6:28277054..28279277-chr6:28294657..28297286,2	K562	blood:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10456362	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1076639	0.87[ASN][1000 genomes]
rs11965538	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13200462	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1419183	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1679709	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1679732	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1778508	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1778511	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1936365	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs213239	0.83[ASN][1000 genomes]
rs213241	0.83[ASN][1000 genomes]
rs213243	0.83[ASN][1000 genomes]
rs213244	0.84[ASN][1000 genomes]
rs2743554	0.87[ASN][1000 genomes]
rs2743555	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2799077	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2799079	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs68141011	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6905391	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs735765	0.84[EUR][1000 genomes]
rs7740487	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs853676	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs853678	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs853679	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs853681	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs853685	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs853687	0.87[ASN][1000 genomes]
rs853688	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs853694	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9468342	0.87[ASN][1000 genomes]
rs9468345	0.83[ASN][1000 genomes]
rs9986596	0.90[EUR][1000 genomes];0.83[ASN][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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs853682	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs853682	OR2B8P	cis	Thyroid	GTEx
rs853682	RP5-874C20.3	cis	Thyroid	GTEx
rs853682	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs853682	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs853682	AL022393.7	cis	Muscle Skeletal	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28288200-28299200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:28290800-28298200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr6:28291400-28298000	ZNF genes & repeats	Liver	Liver
4	chr6:28291600-28296000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:28292600-28297200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
6	chr6:28294800-28302000	Weak transcription	HepG2	liver
7	chr6:28294800-28302800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:28295000-28296000	Strong transcription	Brain Cingulate Gyrus	brain
9	chr6:28295400-28296600	Weak transcription	Fetal Intestine Large	intestine
10	chr6:28295400-28296600	Weak transcription	Fetal Stomach	stomach
11	chr6:28295400-28296600	Weak transcription	Pancreas	Pancrea
12	chr6:28295400-28296800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:28295400-28296800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:28295400-28296800	Weak transcription	Esophagus	oesophagus
15	chr6:28295400-28296800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:28295400-28296800	Weak transcription	Gastric	stomach
17	chr6:28295400-28297000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr6:28295400-28301400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:28295400-28302400	Weak transcription	Brain Angular Gyrus	brain
20	chr6:28295400-28302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr6:28295400-28303000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:28295400-28303000	Weak transcription	Thymus	Thymus
23	chr6:28295600-28296600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:28295600-28296600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:28295600-28296600	Weak transcription	Colonic Mucosa	Colon
26	chr6:28295600-28296600	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:28295600-28296600	Weak transcription	Ovary	ovary
28	chr6:28295600-28296600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr6:28295600-28296800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:28295600-28296800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:28295600-28296800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:28295600-28296800	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:28295600-28296800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:28295600-28296800	Weak transcription	Psoas Muscle	Psoas
35	chr6:28295600-28296800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:28295600-28296800	Weak transcription	Right Ventricle	heart
37	chr6:28295600-28296800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr6:28295600-28297000	Weak transcription	Brain Anterior Caudate	brain
39	chr6:28295600-28297000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr6:28295600-28297200	Weak transcription	Fetal Brain Female	brain
41	chr6:28295600-28297800	Weak transcription	K562	blood
42	chr6:28295600-28302000	Weak transcription	Fetal Heart	heart
43	chr6:28295600-28302200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:28295600-28302200	Weak transcription	Hela-S3	cervix
45	chr6:28295600-28302400	Weak transcription	Brain Substantia Nigra	brain
46	chr6:28295600-28302600	Weak transcription	Stomach Mucosa	stomach
47	chr6:28295600-28302800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:28295600-28302800	Weak transcription	Fetal Brain Male	brain
49	chr6:28295800-28296400	Weak transcription	Left Ventricle	heart
50	chr6:28295800-28296600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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