Variant report

Variant	rs974962
Chromosome Location	chr6:30314607-30314608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr6:30314400-30314685	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:30311254-30314649	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30178310..30184484-chr6:30311860..30320436,13	MCF-7	breast:
2	chr20:55838873..55840993-chr6:30313290..30315542,2	MCF-7	breast:
3	chr6:30188017..30189614-chr6:30314561..30316760,2	MCF-7	breast:
4	chr6:30170658..30173210-chr6:30313081..30315587,2	K562	blood:
5	chr6:30314566..30317004-chr6:30328728..30331075,2	MCF-7	breast:
6	chr6:30293058..30297784-chr6:30308514..30315279,24	MCF-7	breast:

No data

Variant related genes	Relation type
HLA-N	TF binding region
ENSG00000234127	Chromatin interaction
ENSG00000231074	Chromatin interaction
ENSG00000248167	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000270604	Chromatin interaction
ENSG00000204599	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12174823	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1579218	0.91[EUR][1000 genomes]
rs1579219	0.91[EUR][1000 genomes]
rs2187980	0.84[ASN][1000 genomes]
rs2240058	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2285798	0.91[EUR][1000 genomes]
rs2394779	0.91[EUR][1000 genomes]
rs2894145	0.91[EUR][1000 genomes]
rs3778626	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5030611	0.84[EUR][1000 genomes]
rs56183729	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9295844	0.91[EUR][1000 genomes]
rs9357095	0.91[EUR][1000 genomes]
rs9366755	0.91[EUR][1000 genomes]
rs9368628	0.90[EUR][1000 genomes]
rs9368632	0.91[EUR][1000 genomes]
rs9368633	0.91[EUR][1000 genomes]
rs9380173	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9391679	0.91[EUR][1000 genomes]
rs9391762	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9391806	0.91[EUR][1000 genomes]
rs9391807	0.91[EUR][1000 genomes]
rs9393999	0.91[EUR][1000 genomes]
rs9394000	0.91[EUR][1000 genomes]
rs9394002	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9405046	0.82[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	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs974962	TRIM26	Cis_1M	lymphoblastoid	RTeQTL
rs974962	RPP21	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30313400-30321400	Weak transcription	Spleen	Spleen
2	chr6:30313800-30316400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:30313800-30325600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:30314000-30314800	Strong transcription	HSMMtube	muscle
5	chr6:30314000-30315000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:30314000-30315000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:30314000-30315400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:30314000-30316400	Weak transcription	Adipose Nuclei	Adipose
9	chr6:30314000-30316400	Strong transcription	Thymus	Thymus
10	chr6:30314000-30316800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:30314000-30317200	Weak transcription	Brain Substantia Nigra	brain
12	chr6:30314000-30318000	Weak transcription	Fetal Kidney	kidney
13	chr6:30314000-30318400	Weak transcription	HSMM	muscle
14	chr6:30314000-30319400	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:30314000-30319400	Weak transcription	Colonic Mucosa	Colon
16	chr6:30314000-30323200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:30314000-30323200	Weak transcription	Aorta	Aorta
18	chr6:30314000-30324200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr6:30314000-30325600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:30314200-30314800	Weak transcription	Gastric	stomach
21	chr6:30314200-30314800	Strong transcription	NHLF	lung
22	chr6:30314200-30315000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:30314200-30315000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:30314200-30315000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr6:30314200-30315000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:30314200-30315000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr6:30314200-30315000	Strong transcription	Primary hematopoietic stem cells	blood
28	chr6:30314200-30315000	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr6:30314200-30315000	Strong transcription	Fetal Thymus	thymus
30	chr6:30314200-30315000	Strong transcription	Ovary	ovary
31	chr6:30314200-30315000	Strong transcription	HMEC	breast
32	chr6:30314200-30315200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:30314200-30315200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:30314200-30315200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr6:30314200-30315200	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr6:30314200-30315200	Strong transcription	Brain Cingulate Gyrus	brain
37	chr6:30314200-30315200	Strong transcription	Placenta	Placenta
38	chr6:30314200-30315400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:30314200-30315400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:30314200-30315400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:30314200-30315400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr6:30314200-30315400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr6:30314200-30315600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:30314200-30315600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr6:30314200-30315600	Strong transcription	Primary B cells from cord blood	blood
46	chr6:30314200-30315600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:30314200-30315600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr6:30314200-30315600	Strong transcription	Fetal Muscle Trunk	muscle
49	chr6:30314200-30315600	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr6:30314200-30315600	Strong transcription	Skeletal Muscle Female	skeletal muscle

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