Variant report

Variant	rs57894361
Chromosome Location	chr6:150186524-150186525
allele	A/T
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	RAD21	chr6:150183910-150186688	SK-N-SH	brain:	n/a	chr6:150184360-150184374 chr6:150185705-150185718 chr6:150185250-150185264
2	CTCF	chr6:150186480-150186630	HCT-116	colon:	n/a	n/a
3	MAX	chr6:150184113-150186548	HCT-116	colon:	n/a	chr6:150185270-150185280
4	RAD21	chr6:150184847-150186654	HCT-116	colon:	n/a	chr6:150185705-150185718 chr6:150185250-150185264
5	CTCF	chr6:150186420-150186570	GM12873	blood:	n/a	n/a
6	MXI1	chr6:150183904-150186614	SK-N-SH	brain:	n/a	n/a
7	RAD21	chr6:150185928-150186614	MCF-7	breast:	n/a	n/a
8	CTCF	chr6:150185855-150186720	A549	lung:	n/a	n/a
9	CTCF	chr6:150185950-150186652	HCT-116	colon:	n/a	n/a
10	RAD21	chr6:150185950-150186537	A549	lung:	n/a	n/a
11	RAD21	chr6:150186068-150186559	ECC-1	luminal epithelium:	n/a	n/a
12	ZC3H11A	chr6:150186206-150186618	K562	blood:	n/a	n/a
13	RAD21	chr6:150185168-150186582	HCT-116	colon:	n/a	chr6:150185705-150185718 chr6:150185250-150185264
14	MAZ	chr6:150183983-150186584	IMR90	lung:	n/a	chr6:150185270-150185280
15	CTCF	chr6:150184074-150186891	SK-N-SH	brain:	n/a	chr6:150185422-150185435
16	SMC3	chr6:150183916-150186608	SK-N-SH	brain:	n/a	chr6:150185239-150185249
17	CTCF	chr6:150186520-150186670	GM06990	blood:	n/a	n/a
18	CTCF	chr6:150186035-150186641	IMR90	lung:	n/a	n/a
19	REST	chr6:150183977-150186692	H1-neurons	neurons:	n/a	chr6:150185423-150185436 chr6:150185591-150185604 chr6:150185692-150185705
20	CTCF	chr6:150185966-150186568	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:150156036..150158963-chr6:150184147..150187311,3	MCF-7	breast:
2	chr6:150183161..150188305-chr6:150206346..150214162,9	MCF-7	breast:
3	chr6:150184661..150189239-chr6:150198084..150201371,4	MCF-7	breast:
4	chr6:150185187..150186828-chr6:150215109..150217579,2	MCF-7	breast:
5	chr6:150186409..150189034-chr6:150239066..150241266,2	MCF-7	breast:
6	chr6:150037040..150038886-chr6:150185486..150187035,2	K562	blood:
7	chr6:150186302..150188604-chr6:150204580..150207263,3	MCF-7	breast:
8	chr6:150181490..150187274-chr6:150243970..150248410,8	MCF-7	breast:
9	chr6:149865631..149868201-chr6:150184694..150186592,2	MCF-7	breast:

Variant related genes	Relation type
LRP11	TF binding region
ENSG00000223701	Chromatin interaction
ENSG00000217733	Chromatin interaction
ENSG00000131023	Chromatin interaction
ENSG00000164520	Chromatin interaction
ENSG00000203722	Chromatin interaction
ENSG00000120256	Chromatin interaction
ENSG00000131013	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10457852	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12204653	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12209310	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12210822	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12527391	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12528243	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1855572	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1999632	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1999633	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2342766	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3798763	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3922946	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3922947	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4869755	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4869756	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4869767	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4869768	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4870078	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4870117	0.83[AMR][1000 genomes]
rs4870118	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5024811	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6557165	0.83[EUR][1000 genomes]
rs6912330	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6925151	0.86[EUR][1000 genomes]
rs7452592	0.84[EUR][1000 genomes]
rs7764677	0.84[EUR][1000 genomes]
rs915140	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9322229	0.84[EUR][1000 genomes]
rs9371228	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9383941	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9397070	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv3437961	chr6:150182459-150187257	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs57894361	RAET1G	cis	Thyroid	GTEx
rs57894361	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs57894361	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs57894361	RP11-350J20.5	cis	Artery Tibial	GTEx
rs57894361	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs57894361	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs57894361	RP11-350J20.5	cis	Esophagus Mucosa	GTEx
rs57894361	RP11-350J20.5	cis	lung	GTEx
rs57894361	C6orf72	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150183600-150186600	Active TSS	Brain Angular Gyrus	brain
2	chr6:150183800-150186600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:150184200-150186600	Active TSS	Brain Hippocampus Middle	brain
4	chr6:150184200-150186600	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr6:150185800-150186600	Enhancers	Liver	Liver
6	chr6:150185800-150189200	Weak transcription	Gastric	stomach
7	chr6:150186000-150186600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:150186000-150189200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:150186200-150186600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:150186200-150186600	Enhancers	Fetal Brain Male	brain
11	chr6:150186200-150186600	Enhancers	Fetal Muscle Leg	muscle
12	chr6:150186200-150186600	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr6:150186200-150186600	Enhancers	Dnd41	blood
14	chr6:150186200-150186600	Enhancers	Hela-S3	cervix
15	chr6:150186200-150186600	Enhancers	HepG2	liver
16	chr6:150186200-150186600	Enhancers	HMEC	breast
17	chr6:150186200-150186600	Enhancers	NHDF-Ad	bronchial
18	chr6:150186200-150188800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr6:150186200-150189000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:150186200-150189000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:150186200-150189000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:150186200-150189000	Weak transcription	NHLF	lung
23	chr6:150186200-150189200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:150186200-150189200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:150186200-150189200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:150186200-150189200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:150186200-150189200	Weak transcription	NHEK	skin
28	chr6:150186200-150189400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:150186200-150189600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:150186200-150189600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:150186200-150189800	Weak transcription	Ovary	ovary
32	chr6:150186200-150190000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:150186200-150194400	Weak transcription	Pancreas	Pancrea
34	chr6:150186400-150186600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:150186400-150186600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr6:150186400-150186600	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr6:150186400-150186600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:150186400-150186600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:150186400-150186600	Enhancers	Adipose Nuclei	Adipose
40	chr6:150186400-150186600	Enhancers	Brain Anterior Caudate	brain
41	chr6:150186400-150186600	Flanking Active TSS	A549	lung
42	chr6:150186400-150187800	Enhancers	K562	blood
43	chr6:150186400-150189000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr6:150186400-150189000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr6:150186400-150189000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr6:150186400-150189000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:150186400-150189000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:150186400-150189000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:150186400-150189400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr6:150186400-150189400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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