Variant report

Variant	rs853694
Chromosome Location	chr6:28279100-28279101
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28278749..28286420-chr6:28298924..28309589,20	K562	blood:
2	chr6:28278690..28281090-chr6:28292415..28293983,2	K562	blood:
3	chr6:28278744..28280710-chr6:28315124..28318113,2	K562	blood:
4	chr6:28277054..28279277-chr6:28294657..28297286,2	K562	blood:

Variant related genes	Relation type
ENSG00000189298	Chromatin interaction
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10456362	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1076639	0.86[ASN][1000 genomes]
rs11755032	0.89[ASN][1000 genomes]
rs11965538	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13200462	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1339899	0.87[ASN][1000 genomes]
rs1419183	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1679709	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1679732	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1778507	0.86[ASN][1000 genomes]
rs1778508	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1778511	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1936365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs213239	0.82[ASN][1000 genomes]
rs213241	0.82[ASN][1000 genomes]
rs213243	0.82[ASN][1000 genomes]
rs213244	0.83[ASN][1000 genomes]
rs2743554	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2743555	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2799077	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2799079	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68141011	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6905391	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6920512	0.84[ASN][1000 genomes]
rs735765	0.85[EUR][1000 genomes]
rs7740487	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs853676	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853678	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853679	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853681	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853682	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs853685	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853687	0.86[ASN][1000 genomes]
rs853688	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9461446	0.86[ASN][1000 genomes]
rs9461448	0.89[ASN][1000 genomes]
rs9461449	0.89[ASN][1000 genomes]
rs9468321	0.86[ASN][1000 genomes]
rs9468322	0.86[ASN][1000 genomes]
rs9468342	0.86[ASN][1000 genomes]
rs9468345	0.82[ASN][1000 genomes]
rs9986596	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[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
rs853694	OR2B8P	cis	Thyroid	GTEx
rs853694	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs853694	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs853694	AL022393.7	cis	Muscle Skeletal	GTEx
rs853694	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs853694	RP5-874C20.3	cis	Thyroid	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28250000-28293800	Weak transcription	Gastric	stomach
2	chr6:28250600-28280600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:28255200-28283000	Weak transcription	HSMMtube	muscle
4	chr6:28255200-28293800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:28256600-28280800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:28265000-28280600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:28268400-28280600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:28268800-28293400	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:28269200-28291600	Weak transcription	Right Ventricle	heart
10	chr6:28269400-28280800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr6:28269800-28280000	Weak transcription	Left Ventricle	heart
12	chr6:28270000-28280800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:28270000-28290400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:28270000-28291400	Weak transcription	Ovary	ovary
15	chr6:28270000-28291600	Weak transcription	Brain Anterior Caudate	brain
16	chr6:28270000-28291600	Weak transcription	Fetal Brain Female	brain
17	chr6:28270000-28293400	Weak transcription	Brain Angular Gyrus	brain
18	chr6:28270400-28279600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:28271200-28293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:28271400-28293400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:28272400-28279200	Weak transcription	K562	blood
22	chr6:28272400-28291800	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:28272400-28293200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:28272600-28292000	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:28272600-28292600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:28272600-28292600	Weak transcription	Brain Germinal Matrix	brain
27	chr6:28273000-28291600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:28276800-28279400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr6:28277000-28279400	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr6:28278000-28279200	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr6:28278400-28280000	Enhancers	HepG2	liver
32	chr6:28278600-28279200	ZNF genes & repeats	Esophagus	oesophagus
33	chr6:28278600-28279400	ZNF genes & repeats	Aorta	Aorta
34	chr6:28278600-28279400	Enhancers	Fetal Intestine Large	intestine
35	chr6:28278600-28279400	ZNF genes & repeats	Pancreas	Pancrea
36	chr6:28278600-28279600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:28278800-28279400	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr6:28278800-28279400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:28278800-28279400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:28278800-28279400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:28278800-28279400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
42	chr6:28278800-28279400	Enhancers	NHDF-Ad	bronchial
43	chr6:28278800-28279400	Enhancers	NHEK	skin
44	chr6:28278800-28279600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:28278800-28279600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:28278800-28279600	Enhancers	GM12878-XiMat	blood
47	chr6:28279000-28279400	Enhancers	HMEC	breast
48	chr6:28279000-28279800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:28279000-28279800	ZNF genes & repeats	Fetal Intestine Small	intestine

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