Variant report

Variant	rs1570335
Chromosome Location	chr1:168877171-168877172
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:168810232..168812979-chr1:168875337..168877595,2	MCF-7	breast:
2	chr1:168875686..168878179-chr1:168887956..168889828,4	MCF-7	breast:
3	chr1:168875687..168879217-chr1:168890314..168893830,4	MCF-7	breast:
4	chr1:168875296..168877977-chr1:169036497..169038451,2	MCF-7	breast:
5	chr1:168869501..168872065-chr1:168874291..168877182,3	MCF-7	breast:
6	chr1:168873646..168880836-chr1:169073615..169079308,19	MCF-7	breast:
7	chr1:168872791..168875183-chr1:168876465..168878195,2	MCF-7	breast:
8	chr1:168875814..168878079-chr1:168940706..168942941,2	MCF-7	breast:
9	chr1:168876521..168880322-chr1:168881956..168884576,3	MCF-7	breast:
10	chr1:168872707..168877840-chr1:169073874..169079301,15	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NME7-1	chr1:168877097-168877208	ENSG00000203601.3

No data

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction
ENSG00000252987	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1022789	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1028642	0.82[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10489364	1.00[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10800393	0.83[CHB][hapmap];0.89[TSI][hapmap]
rs10800395	0.95[ASN][1000 genomes]
rs10919011	0.87[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10919013	0.83[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1885558	0.86[ASN][1000 genomes]
rs2065129	0.88[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2146205	0.83[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs34408738	0.87[ASN][1000 genomes]
rs4142003	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4656166	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427157	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427159	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657987	0.88[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6670083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6670091	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72695643	0.86[ASN][1000 genomes]
rs7514435	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7527859	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551577	0.87[CEU][hapmap]

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	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	nsv437258	chr1:168824111-168890420	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1570335	POGK	cis	cerebellum	SCAN
rs1570335	XCL1	cis	parietal	SCAN
rs1570335	MAEL	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168875000-168877200	Enhancers	Pancreas	Pancrea
2	chr1:168875000-168878000	Enhancers	HepG2	liver
3	chr1:168875400-168877600	Enhancers	Stomach Mucosa	stomach
4	chr1:168875600-168877200	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr1:168875600-168877200	Enhancers	Small Intestine	intestine
6	chr1:168875800-168877200	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr1:168875800-168877800	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr1:168876200-168877400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:168876400-168877200	Enhancers	Brain Hippocampus Middle	brain
10	chr1:168876400-168877200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:168876400-168877400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr1:168876400-168877400	Enhancers	Fetal Intestine Large	intestine
13	chr1:168876400-168878000	Enhancers	Fetal Lung	lung
14	chr1:168876400-168878200	Enhancers	Fetal Kidney	kidney
15	chr1:168876600-168877200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:168876600-168877200	Enhancers	Esophagus	oesophagus
17	chr1:168876600-168878000	Enhancers	Adipose Nuclei	Adipose
18	chr1:168876800-168877200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:168876800-168877200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:168876800-168877200	Enhancers	Fetal Muscle Leg	muscle
21	chr1:168876800-168877200	Enhancers	Placenta	Placenta
22	chr1:168876800-168877400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:168876800-168877600	Enhancers	HSMMtube	muscle
24	chr1:168877000-168877400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:168877000-168877800	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links