Variant report

Variant	rs9366752
Chromosome Location	chr6:30024677-30024678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30023200..30024877-chr6:30024886..30026414,2	MCF-7	breast:
2	chr6:29579503..29582093-chr6:30024357..30026133,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF39-4	chr6:30024530-30025494	ENSG00000204623

Variant related genes	Relation type
ENSG00000204681	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10947050	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11752303	0.81[AMR][1000 genomes]
rs12200084	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2275855	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33959627	0.91[AFR][1000 genomes]
rs3807031	0.91[AFR][1000 genomes]
rs3910312	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711206	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711207	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711209	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4713274	0.81[AMR][1000 genomes]
rs4713275	0.81[AMR][1000 genomes]
rs4713279	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4713281	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4947244	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4959040	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6457127	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7766469	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295825	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9295826	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295829	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295830	0.87[AFR][1000 genomes]
rs9348835	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357092	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9366750	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9380150	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9393986	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393987	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9393988	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9393989	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9405044	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9366752	ZKSCAN3	cis	cerebellum	SCAN
rs9366752	ZNF184	cis	cerebellum	SCAN
rs9366752	ZNF165	cis	cerebellum	SCAN
rs9366752	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs9366752	HLA-A	cis	lymphoblastoid	seeQTL
rs9366752	HCG4P6	Cis_1M	lymphoblastoid	RTeQTL
rs9366752	HLA.A29.1	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29975200-30027800	Weak transcription	Aorta	Aorta
2	chr6:29975600-30027800	Weak transcription	Right Ventricle	heart
3	chr6:29975800-30027800	Weak transcription	Gastric	stomach
4	chr6:29977200-30027600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:29977200-30027800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:29979000-30027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:29979800-30027800	Weak transcription	Pancreas	Pancrea
8	chr6:29987800-30024800	Weak transcription	Fetal Intestine Large	intestine
9	chr6:29988200-30027800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:29988200-30027800	Weak transcription	Esophagus	oesophagus
11	chr6:29988400-30027800	Weak transcription	Thymus	Thymus
12	chr6:29988600-30027400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:29998000-30027600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr6:29999200-30027200	Weak transcription	Fetal Heart	heart
15	chr6:30000000-30027400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr6:30001200-30025000	Weak transcription	Fetal Lung	lung
17	chr6:30001200-30027800	Weak transcription	Fetal Kidney	kidney
18	chr6:30001800-30024800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:30003000-30027200	Weak transcription	Dnd41	blood
20	chr6:30006200-30027600	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:30011000-30027800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:30012400-30027400	Weak transcription	HepG2	liver
23	chr6:30012600-30024800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:30012600-30024800	Weak transcription	HSMM	muscle
25	chr6:30012600-30027200	Weak transcription	HMEC	breast
26	chr6:30012600-30027800	Weak transcription	Small Intestine	intestine
27	chr6:30012800-30027600	Weak transcription	NHDF-Ad	bronchial
28	chr6:30012800-30027800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:30012800-30027800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:30013000-30027400	Weak transcription	NHEK	skin
31	chr6:30013000-30027400	Weak transcription	NHLF	lung
32	chr6:30013000-30027600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:30013400-30027600	Weak transcription	NH-A	brain
34	chr6:30013600-30027600	Weak transcription	Hela-S3	cervix
35	chr6:30013600-30027800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr6:30013600-30027800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:30013800-30025400	Weak transcription	Psoas Muscle	Psoas
38	chr6:30013800-30027200	Weak transcription	GM12878-XiMat	blood
39	chr6:30014000-30028000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr6:30015400-30025000	Weak transcription	K562	blood
41	chr6:30015600-30025000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr6:30015600-30027400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:30015600-30027600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:30016000-30027800	Weak transcription	Spleen	Spleen
45	chr6:30016800-30027400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:30017000-30027600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr6:30017400-30028400	Weak transcription	Lung	lung
48	chr6:30018000-30027600	Weak transcription	Brain Germinal Matrix	brain
49	chr6:30018800-30027200	Weak transcription	Osteobl	bone
50	chr6:30020000-30024800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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