Variant report

Variant	rs6900042
Chromosome Location	chr6:30289271-30289272
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	chr6:30285811..30291810-chr6:30292950..30295041,8	MCF-7	breast:
2	chr6:30280311..30284276-chr6:30285910..30291583,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270604	Chromatin interaction
ENSG00000204599	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	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12055553	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192505	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1264617	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1264618	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1264619	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2187979	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2428506	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2428507	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2516696	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2516708	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2516715	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2523740	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs261947	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844759	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844760	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2844762	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2844764	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2844766	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4711213	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906180	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912771	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913293	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924282	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6924453	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931387	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295842	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357097	0.93[EUR][1000 genomes]
rs9357098	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9368635	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380167	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380172	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6900042	TRIM26	Cis_1M	lymphoblastoid	RTeQTL
rs6900042	HCG18	cis	normal skin	skin_eQTL
rs6900042	HCG18	Cis_1M	lymphoblastoid	RTeQTL
rs6900042	LOC401245	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 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	chr6:30262600-30292400	Weak transcription	Pancreas	Pancrea
4	chr6:30262800-30290200	Weak transcription	Spleen	Spleen
5	chr6:30263000-30293000	Weak transcription	Brain Substantia Nigra	brain
6	chr6:30264200-30289800	Weak transcription	Gastric	stomach
7	chr6:30270600-30292600	Weak transcription	Esophagus	oesophagus
8	chr6:30270800-30292200	Weak transcription	NHDF-Ad	bronchial
9	chr6:30271000-30292400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:30271000-30292800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:30271400-30291400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:30272200-30292200	Weak transcription	Fetal Brain Male	brain
13	chr6:30272400-30289600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:30274600-30292200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:30274600-30292600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:30275400-30293400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:30278200-30292400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:30280000-30289400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr6:30280000-30290400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:30280400-30292800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr6:30280800-30292000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr6:30281200-30292200	Weak transcription	Fetal Brain Female	brain
23	chr6:30281800-30292000	Weak transcription	Brain Hippocampus Middle	brain
24	chr6:30281800-30292600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr6:30282000-30292000	Weak transcription	Fetal Lung	lung
26	chr6:30282000-30292400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:30282200-30289800	Weak transcription	Brain Angular Gyrus	brain
28	chr6:30282200-30290200	Weak transcription	Left Ventricle	heart
29	chr6:30282200-30290200	Weak transcription	HMEC	breast
30	chr6:30282200-30291000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:30282200-30292200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:30282200-30292400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:30282200-30292400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:30282200-30292600	Weak transcription	Right Ventricle	heart
35	chr6:30282200-30292800	Weak transcription	Brain Anterior Caudate	brain
36	chr6:30282200-30292800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:30282200-30292800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:30282400-30291000	Weak transcription	Brain Germinal Matrix	brain
39	chr6:30282600-30292400	Weak transcription	Psoas Muscle	Psoas
40	chr6:30284200-30290200	Weak transcription	Ovary	ovary
41	chr6:30284200-30292400	Weak transcription	Colonic Mucosa	Colon
42	chr6:30284400-30289800	Weak transcription	NHLF	lung
43	chr6:30284400-30290200	Weak transcription	Placenta	Placenta
44	chr6:30284400-30293000	Weak transcription	Aorta	Aorta
45	chr6:30284600-30289800	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr6:30284600-30289800	Weak transcription	NH-A	brain
47	chr6:30284600-30292400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr6:30284600-30292800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr6:30284600-30292800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr6:30284800-30292000	Weak transcription	Duodenum Mucosa	Duodenum

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