Variant report

Variant	rs9380167
Chromosome Location	chr6:30274461-30274462
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30274161-30274576	K562	blood:	n/a	n/a
2	CTCF	chr6:30274320-30274470	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:30274379-30274637	K562	blood:	n/a	n/a
4	POLR2A	chr6:30274423-30274560	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30258650..30265091-chr6:30270138..30274799,6	MCF-7	breast:
2	chr6:30256199..30257917-chr6:30272778..30275298,2	MCF-7	breast:
3	chr6:30273472..30275726-chr6:30312691..30314327,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM26-2	chr6:30271848-30274737	ENSG00000231074.4

No data

Variant related genes	Relation type
HCG18	TF binding region
ENSG00000241370	Chromatin interaction
ENSG00000231074	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1075105	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12055553	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192505	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1264617	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1264618	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1264619	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2187979	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2428506	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2428507	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2516696	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2516708	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2516715	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2523740	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs261947	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844759	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844760	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844762	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2844764	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2844766	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4711213	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900042	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906180	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912771	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924282	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6924453	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931387	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295842	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357097	0.93[EUR][1000 genomes]
rs9357098	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9368635	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380172	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9380167	HCG18	Cis_1M	lymphoblastoid	RTeQTL
rs9380167	LOC401245	cis	multi-tissue	Pritchard
rs9380167	HCG18	cis	normal skin	skin_eQTL
rs9380167	TRIM26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30256200-30292000	Weak transcription	Fetal Heart	heart
2	chr6:30257600-30292800	Weak transcription	Fetal Kidney	kidney
3	chr6:30259000-30287200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:30262600-30279200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:30262600-30279600	Weak transcription	Small Intestine	intestine
6	chr6:30262600-30292400	Weak transcription	Pancreas	Pancrea
7	chr6:30262800-30280200	Weak transcription	HUVEC	blood vessel
8	chr6:30262800-30280400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:30262800-30283200	Weak transcription	NHLF	lung
10	chr6:30262800-30290200	Weak transcription	Spleen	Spleen
11	chr6:30263000-30277200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:30263000-30280000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:30263000-30281400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:30263000-30282000	Weak transcription	Psoas Muscle	Psoas
15	chr6:30263000-30293000	Weak transcription	Brain Substantia Nigra	brain
16	chr6:30263200-30280200	Weak transcription	HSMMtube	muscle
17	chr6:30263200-30280600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr6:30263200-30281600	Weak transcription	Right Ventricle	heart
19	chr6:30263800-30280800	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:30264000-30280800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:30264200-30280200	Weak transcription	NH-A	brain
22	chr6:30264200-30286600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:30264200-30289800	Weak transcription	Gastric	stomach
24	chr6:30264400-30285200	Weak transcription	Colon Smooth Muscle	Colon
25	chr6:30266000-30275400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:30268200-30277800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
27	chr6:30268600-30278200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:30268600-30278600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:30269000-30274600	Strong transcription	HSMM	muscle
30	chr6:30269000-30275000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:30269000-30277800	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr6:30269000-30278200	Strong transcription	HepG2	liver
33	chr6:30269000-30278600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:30269200-30274600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr6:30269200-30285800	Strong transcription	Dnd41	blood
36	chr6:30269600-30274600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr6:30270400-30283800	Weak transcription	Colonic Mucosa	Colon
38	chr6:30270600-30278200	Strong transcription	NHEK	skin
39	chr6:30270600-30279600	Weak transcription	Left Ventricle	heart
40	chr6:30270600-30292600	Weak transcription	Esophagus	oesophagus
41	chr6:30270800-30277200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr6:30270800-30278200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr6:30270800-30279200	Weak transcription	Adipose Nuclei	Adipose
44	chr6:30270800-30280200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:30270800-30281600	Weak transcription	Fetal Lung	lung
46	chr6:30270800-30292200	Weak transcription	NHDF-Ad	bronchial
47	chr6:30271000-30275000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:30271000-30275400	Strong transcription	A549	lung
49	chr6:30271000-30276800	Weak transcription	Liver	Liver
50	chr6:30271000-30277400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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