Variant report

Variant	rs6912239
Chromosome Location	chr6:30291152-30291153
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr6:30291019-30291326	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:30290964-30291242	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30238145..30240956-chr6:30290362..30292756,2	MCF-7	breast:
2	chr6:30289552..30291696-chr6:30311797..30314198,2	MCF-7	breast:
3	chr6:30285811..30291810-chr6:30292950..30295041,8	MCF-7	breast:
4	chr6:30280311..30284276-chr6:30285910..30291583,5	MCF-7	breast:

Variant related genes	Relation type
TRIM39	TF binding region
ENSG00000204599	Chromatin interaction
ENSG00000241370	Chromatin interaction
ENSG00000231074	Chromatin interaction
ENSG00000270604	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1045251	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1060065	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1264616	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1579218	0.80[ASN][1000 genomes]
rs1579219	0.80[ASN][1000 genomes]
rs2023476	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2023477	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2023478	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2057727	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074474	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2097773	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2285798	0.82[ASN][1000 genomes]
rs2394779	0.83[ASN][1000 genomes]
rs2394780	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2508026	0.81[EUR][1000 genomes]
rs2516697	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2516699	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516700	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516702	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516704	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516705	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516706	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516707	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516710	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516713	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2516718	0.81[AFR][1000 genomes]
rs2523737	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2523744	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523745	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523746	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523747	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523748	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523750	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs261943	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs261948	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs261949	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28360021	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28360023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844752	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844761	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2844763	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844765	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2894145	0.81[ASN][1000 genomes]
rs3778624	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778626	0.81[ASN][1000 genomes]
rs6904208	0.87[AFR][1000 genomes]
rs6912495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7452694	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7767653	0.83[AFR][1000 genomes]
rs7767817	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295843	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295844	0.83[ASN][1000 genomes]
rs9357095	0.83[ASN][1000 genomes]
rs9366755	0.82[ASN][1000 genomes]
rs9368628	0.83[ASN][1000 genomes]
rs9368632	0.83[ASN][1000 genomes]
rs9368633	0.83[ASN][1000 genomes]
rs9380168	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380174	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9391679	0.83[ASN][1000 genomes]
rs9391806	0.83[ASN][1000 genomes]
rs9391807	0.83[ASN][1000 genomes]
rs9393999	0.83[ASN][1000 genomes]
rs9394000	0.83[ASN][1000 genomes]
rs9394001	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394002	0.81[ASN][1000 genomes]
rs9394003	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs962899	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs974963	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6912239	HCG18	Cis_1M	lymphoblastoid	RTeQTL
rs6912239	TRIM26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 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	chr6:30263000-30293000	Weak transcription	Brain Substantia Nigra	brain
5	chr6:30270600-30292600	Weak transcription	Esophagus	oesophagus
6	chr6:30270800-30292200	Weak transcription	NHDF-Ad	bronchial
7	chr6:30271000-30292400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:30271000-30292800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:30271400-30291400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:30272200-30292200	Weak transcription	Fetal Brain Male	brain
11	chr6:30274600-30292200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:30274600-30292600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:30275400-30293400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:30278200-30292400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:30280400-30292800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr6:30280800-30292000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr6:30281200-30292200	Weak transcription	Fetal Brain Female	brain
18	chr6:30281800-30292000	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:30281800-30292600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:30282000-30292000	Weak transcription	Fetal Lung	lung
21	chr6:30282000-30292400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:30282200-30292200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:30282200-30292400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:30282200-30292400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:30282200-30292600	Weak transcription	Right Ventricle	heart
26	chr6:30282200-30292800	Weak transcription	Brain Anterior Caudate	brain
27	chr6:30282200-30292800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr6:30282200-30292800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:30282600-30292400	Weak transcription	Psoas Muscle	Psoas
30	chr6:30284200-30292400	Weak transcription	Colonic Mucosa	Colon
31	chr6:30284400-30293000	Weak transcription	Aorta	Aorta
32	chr6:30284600-30292400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr6:30284600-30292800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr6:30284600-30292800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:30284800-30292000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr6:30285200-30292800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr6:30285200-30293000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:30285200-30293000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr6:30285400-30292800	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr6:30286000-30292800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr6:30286400-30291600	Weak transcription	Fetal Intestine Large	intestine
42	chr6:30286400-30292200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr6:30286800-30292400	Weak transcription	Lung	lung
44	chr6:30287200-30292400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:30287200-30292400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr6:30287200-30292600	Weak transcription	Fetal Muscle Leg	muscle
47	chr6:30287400-30291200	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr6:30287400-30292400	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr6:30287600-30292200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr6:30287600-30292200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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