Variant report

Variant	rs6806356
Chromosome Location	chr3:48727636-48727637
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48723848-48729026	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:48727621-48728944	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:48727507-48728153	GM12891	blood:	n/a	n/a
4	POLR2A	chr3:48727435-48728041	GM12892	blood:	n/a	n/a
5	POLR2A	chr3:48724618-48727829	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:48723418-48727664	A549	lung:	n/a	n/a
7	POLR2A	chr3:48726952-48727760	K562	blood:	n/a	n/a
8	POLR2A	chr3:48727624-48728724	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:48723842-48727720	GM12891	blood:	n/a	n/a
10	POLR2A	chr3:48724167-48728096	GM12892	blood:	n/a	n/a
11	POLR2A	chr3:48727613-48727670	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:48708844..48711305-chr3:48727090..48731325,3	K562	blood:
2	chr3:48720678..48725638-chr3:48726169..48732697,10	MCF-7	breast:
3	chr3:48646300..48647842-chr3:48725796..48728782,2	K562	blood:
4	chr3:48721678..48726571-chr3:48727447..48730865,5	K562	blood:
5	chr3:48725798..48728623-chr3:48730156..48733181,3	K562	blood:
6	chr3:48725665..48728051-chr3:48734995..48736912,2	MCF-7	breast:
7	chr3:48723202..48724922-chr3:48725694..48728328,2	K562	blood:
8	chr3:48725548..48727703-chr3:48731349..48733910,3	K562	blood:

No data

Variant related genes	Relation type
NCKIPSD	TF binding region
ENSG00000213672	Chromatin interaction
ENSG00000068745	Chromatin interaction
ENSG00000271973	Chromatin interaction
ENSG00000010256	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10865953	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12632533	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs14018	1.00[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs4858799	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4858800	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4858830	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974088	1.00[CEU][hapmap];0.80[TSI][hapmap]
rs6442129	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442131	0.82[EUR][1000 genomes]
rs6766238	1.00[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs6796790	1.00[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs6801211	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs72929179	1.00[ASN][1000 genomes]
rs7610519	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641050	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9284885	1.00[CEU][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap]
rs9311431	1.00[CEU][hapmap]
rs9822485	0.80[LWK][hapmap];0.92[YRI][hapmap]
rs9848268	0.96[EUR][1000 genomes]
rs9859473	1.00[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs9873227	0.85[EUR][1000 genomes]
rs9874010	0.92[YRI][hapmap]
rs9879978	1.00[CEU][hapmap]
rs9882443	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990211	0.82[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS 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	49 gene(s)	inside rSNPs	diseases
4	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv590248	chr3:48716993-48727636	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs6806356	LEPR	trans	lymphoblastoid	RTeQTL
rs6806356	WDR6	cis	parietal	SCAN
rs6806356	AMT	cis	Thyroid	GTEx
rs6806356	CDC25A	cis	cerebellum	SCAN
rs6806356	AMT	cis	Artery Tibial	GTEx
rs6806356	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs6806356	AMT	cis	cerebellum	SCAN
rs6806356	AMT	cis	Adipose Subcutaneous	GTEx
rs6806356	NICN1	cis	cerebellum	SCAN
rs6806356	PHF7	cis	parietal	SCAN
rs6806356	IQCF1	cis	cerebellum	SCAN
rs6806356	AMT	cis	lung	GTEx
rs6806356	NCKIPSD	cis	Nerve Tibial	GTEx
rs6806356	TLR9	cis	parietal	SCAN
rs6806356	NICN1-AS1	cis	Thyroid	GTEx
rs6806356	NCKIPSD	cis	cerebellum	SCAN
rs6806356	NICN1	cis	Thyroid	GTEx
rs6806356	DALRD3	cis	parietal	SCAN
rs6806356	DALRD3	cis	cerebellum	SCAN
rs6806356	P4HTM	cis	parietal	SCAN
rs6806356	WDR6	cis	Muscle Skeletal	GTEx
rs6806356	QRICH1	cis	cerebellum	SCAN
rs6806356	NICN1	cis	parietal	SCAN
rs6806356	NCKIPSD	cis	Muscle Skeletal	GTEx
rs6806356	QARS	cis	parietal	SCAN
rs6806356	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs6806356	AMT	cis	parietal	SCAN
rs6806356	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs6806356	WDR6	cis	cerebellum	SCAN
rs6806356	ZNF589	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48723800-48732200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:48723800-48733800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:48724200-48728400	Weak transcription	Small Intestine	intestine
4	chr3:48724200-48729600	Weak transcription	Stomach Mucosa	stomach
5	chr3:48724200-48729800	Strong transcription	Brain Germinal Matrix	brain
6	chr3:48724200-48730200	Weak transcription	K562	blood
7	chr3:48724200-48732400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:48724200-48732600	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:48724400-48729400	Strong transcription	Brain Hippocampus Middle	brain
10	chr3:48724400-48729600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:48724400-48729800	Strong transcription	HSMM	muscle
12	chr3:48724400-48730400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:48724400-48735800	Strong transcription	GM12878-XiMat	blood
14	chr3:48724600-48729000	Strong transcription	Esophagus	oesophagus
15	chr3:48724600-48729400	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr3:48724600-48729800	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr3:48724600-48730000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:48724600-48730000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:48724600-48730600	Strong transcription	Fetal Brain Female	brain
20	chr3:48724600-48731400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:48724600-48731800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:48724600-48732000	Strong transcription	Fetal Lung	lung
23	chr3:48724600-48732200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:48724600-48732400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:48724600-48732400	Strong transcription	Fetal Intestine Large	intestine
26	chr3:48724600-48733000	Strong transcription	Primary T cells from cord blood	blood
27	chr3:48724600-48734000	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:48724600-48734000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:48724600-48738000	Strong transcription	Thymus	Thymus
30	chr3:48724600-48738400	Strong transcription	Primary hematopoietic stem cells	blood
31	chr3:48724600-48740400	Strong transcription	Primary B cells from cord blood	blood
32	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
33	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:48724800-48727800	Strong transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:48724800-48729800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:48724800-48729800	Strong transcription	Brain Angular Gyrus	brain
37	chr3:48724800-48730000	Strong transcription	Brain Cingulate Gyrus	brain
38	chr3:48724800-48730000	Strong transcription	Brain Substantia Nigra	brain
39	chr3:48724800-48730200	Weak transcription	Right Atrium	heart
40	chr3:48724800-48730200	Strong transcription	HSMMtube	muscle
41	chr3:48724800-48730800	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:48724800-48731000	Strong transcription	Adipose Nuclei	Adipose
43	chr3:48724800-48731200	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:48724800-48731200	Strong transcription	Fetal Kidney	kidney
45	chr3:48724800-48731200	Strong transcription	HUVEC	blood vessel
46	chr3:48724800-48731400	Strong transcription	Aorta	Aorta
47	chr3:48724800-48731600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:48724800-48731600	Strong transcription	Hela-S3	cervix
49	chr3:48724800-48732000	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr3:48724800-48732200	Strong transcription	H1 Cell Line	embryonic stem cell

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