Variant report

Variant	rs1999633
Chromosome Location	chr6:150187712-150187713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr6:150187508-150187767	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:150187701..150190612-chr6:150206560..150208609,2	K562	blood:
2	chr6:150183161..150188305-chr6:150206346..150214162,9	MCF-7	breast:
3	chr6:150184661..150189239-chr6:150198084..150201371,4	MCF-7	breast:
4	chr6:150186409..150189034-chr6:150239066..150241266,2	MCF-7	breast:
5	chr6:150167839..150171816-chr6:150186693..150189063,3	K562	blood:
6	chr2:174828821..174830614-chr6:150186810..150189334,2	MCF-7	breast:
7	chr6:150186302..150188604-chr6:150204580..150207263,3	MCF-7	breast:
8	chr6:150168942..150171816-chr6:150186693..150188431,2	K562	blood:

No data

Variant related genes	Relation type
LRP11	TF binding region
ENSG00000172845	Chromatin interaction
ENSG00000217733	Chromatin interaction
ENSG00000164520	Chromatin interaction
ENSG00000223701	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 16 )

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

rs_ID	r²[population]
rs10457852	0.88[CEU][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12204653	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12209310	0.88[CEU][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12210822	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12527391	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12528243	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1855572	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1999632	0.94[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2342766	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3798763	0.87[CEU][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3922946	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3922947	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4869755	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4869756	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4869767	0.83[CEU][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4869768	0.83[CEU][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4870078	0.88[CEU][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4870117	0.81[AMR][1000 genomes]
rs4870118	0.82[AMR][1000 genomes]
rs5024811	0.83[CEU][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57894361	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6557165	0.88[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs6912330	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6925151	0.88[CEU][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7452592	0.83[EUR][1000 genomes]
rs7764677	0.83[EUR][1000 genomes]
rs7769118	0.80[YRI][hapmap]
rs915140	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9322229	0.88[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs9371228	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9383941	0.88[CEU][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs1999633	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs1999633	RP11-350J20.5	cis	Artery Tibial	GTEx
rs1999633	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs1999633	LATS1	cis	parietal	SCAN
rs1999633	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs1999633	LRP11	cis	parietal	SCAN
rs1999633	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs1999633	RP11-350J20.5	cis	Thyroid	GTEx
rs1999633	RP11-350J20.5	cis	Adipose Subcutaneous	GTEx
rs1999633	SHPRH	cis	cerebellum	SCAN
rs1999633	RP11-350J20.5	cis	lung	GTEx
rs1999633	LATS1	cis	cerebellum	SCAN
rs1999633	LRP11	cis	cerebellum	SCAN
rs1999633	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs1999633	NUP43	cis	multi-tissue	Pritchard
rs1999633	RP11-350J20.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150185800-150189200	Weak transcription	Gastric	stomach
2	chr6:150186000-150189200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:150186200-150188800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:150186200-150189000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:150186200-150189000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:150186200-150189000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:150186200-150189000	Weak transcription	NHLF	lung
8	chr6:150186200-150189200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:150186200-150189200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:150186200-150189200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:150186200-150189200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:150186200-150189200	Weak transcription	NHEK	skin
13	chr6:150186200-150189400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:150186200-150189600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:150186200-150189600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:150186200-150189800	Weak transcription	Ovary	ovary
17	chr6:150186200-150190000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:150186200-150194400	Weak transcription	Pancreas	Pancrea
19	chr6:150186400-150187800	Enhancers	K562	blood
20	chr6:150186400-150189000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr6:150186400-150189000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:150186400-150189000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:150186400-150189000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:150186400-150189000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:150186400-150189000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:150186400-150189400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:150186400-150189400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:150186600-150188200	Weak transcription	Dnd41	blood
29	chr6:150186600-150188800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:150186600-150188800	Weak transcription	HMEC	breast
31	chr6:150186600-150189000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:150186600-150189000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:150186600-150189000	Weak transcription	Hela-S3	cervix
34	chr6:150186600-150189000	Weak transcription	HepG2	liver
35	chr6:150186600-150189000	Weak transcription	NHDF-Ad	bronchial
36	chr6:150186600-150189400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:150186600-150189400	Weak transcription	Liver	Liver
38	chr6:150186800-150189000	Weak transcription	A549	lung

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