Variant report

Variant	rs3845408
Chromosome Location	chr1:180868110-180868111
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180866617..180870349-chr1:180876247..180878371,3	MCF-7	breast:
2	chr1:180868023..180870697-chr1:180871039..180876030,6	K562	blood:
3	chr1:180863020..180866201-chr1:180866515..180869291,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-XPR1-1	chr1:180868088-180869874	XLOC_000478

Variant related genes	Relation type
ENSG00000225857	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10732273	1.00[AFR][1000 genomes]
rs1400038	1.00[AFR][1000 genomes]
rs1515960	1.00[AFR][1000 genomes]
rs2063849	1.00[AFR][1000 genomes]
rs2944260	1.00[AFR][1000 genomes]
rs2944263	1.00[AFR][1000 genomes]
rs3002120	1.00[AFR][1000 genomes]
rs3002122	0.87[AFR][1000 genomes]
rs3013635	1.00[AFR][1000 genomes]
rs3013636	1.00[AFR][1000 genomes]
rs3856061	1.00[AFR][1000 genomes]
rs4651076	1.00[AFR][1000 genomes]
rs4652532	1.00[YRI][hapmap]
rs4652534	1.00[AFR][1000 genomes]
rs6683252	1.00[AFR][1000 genomes]
rs7531753	1.00[AFR][1000 genomes]
rs7535885	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7548808	1.00[AFR][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	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180805800-180881000	Weak transcription	Aorta	Aorta
2	chr1:180824000-180880800	Weak transcription	Right Ventricle	heart
3	chr1:180835800-180870400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:180844200-180872200	Weak transcription	Esophagus	oesophagus
5	chr1:180845800-180869000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:180847400-180875400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:180852000-180870400	Weak transcription	A549	lung
8	chr1:180857600-180869600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:180858400-180870600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:180861200-180880800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:180864600-180870200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:180867000-180868600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:180867200-180868200	Enhancers	Adipose Nuclei	Adipose
14	chr1:180867200-180869200	Enhancers	H9 Cell Line	embryonic stem cell
15	chr1:180867400-180868200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:180867400-180868200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:180867400-180868200	Enhancers	Osteobl	bone
18	chr1:180867400-180868400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr1:180867400-180868400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr1:180867400-180868400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:180867400-180868400	Enhancers	Fetal Lung	lung
22	chr1:180867400-180868600	Enhancers	NHDF-Ad	bronchial
23	chr1:180867400-180868800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:180867400-180868800	Enhancers	Placenta	Placenta
25	chr1:180867400-180869000	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr1:180867400-180869200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr1:180867400-180869200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:180867400-180869200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:180867400-180869600	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr1:180867600-180868400	Enhancers	Fetal Heart	heart
31	chr1:180867600-180868600	Enhancers	Fetal Muscle Leg	muscle
32	chr1:180867600-180868800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:180867600-180868800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:180867600-180869400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:180867600-180869400	Enhancers	Fetal Muscle Trunk	muscle
36	chr1:180867600-180869400	Weak transcription	Pancreas	Pancrea
37	chr1:180867600-180869600	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr1:180867600-180869800	Enhancers	H1 Cell Line	embryonic stem cell
39	chr1:180867600-180869800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:180867800-180868400	Enhancers	Fetal Stomach	stomach
41	chr1:180867800-180868600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:180867800-180869200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:180868000-180868800	Enhancers	Right Atrium	heart
44	chr1:180868000-180869000	Enhancers	Fetal Thymus	thymus
45	chr1:180868000-180870600	Weak transcription	Brain Germinal Matrix	brain
46	chr1:180868000-180878600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links