Variant report

Variant	rs1841655
Chromosome Location	chr1:225819058-225819059
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225817081..225819412-chr1:226067962..226070291,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196187	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12564648	0.81[EUR][1000 genomes]
rs12564687	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12565399	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12566165	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12568642	0.86[EUR][1000 genomes]
rs16845030	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16845040	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1771316	1.00[AMR][1000 genomes]
rs2657568	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2840960	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55899644	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56250189	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58088270	0.92[EUR][1000 genomes]
rs6665838	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7544335	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7548206	0.87[AMR][1000 genomes];0.86[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	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225760000-225820600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:225781000-225825400	Weak transcription	Fetal Stomach	stomach
3	chr1:225807200-225820400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:225809800-225837800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:225810000-225825400	Weak transcription	NHEK	skin
6	chr1:225812800-225824400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:225812800-225825000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:225813400-225824800	Weak transcription	Lung	lung
9	chr1:225813600-225837600	Weak transcription	HUVEC	blood vessel
10	chr1:225813800-225838600	Weak transcription	HMEC	breast
11	chr1:225814200-225819600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr1:225814400-225820400	Weak transcription	HSMM	muscle
13	chr1:225814400-225825200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:225814400-225825400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:225814600-225835800	Weak transcription	HSMMtube	muscle
16	chr1:225815400-225823200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:225815400-225823800	Weak transcription	NH-A	brain
18	chr1:225815600-225819800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:225815600-225822800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:225815600-225825400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:225815600-225830000	Weak transcription	Pancreas	Pancrea
22	chr1:225815800-225819800	Weak transcription	Brain Anterior Caudate	brain
23	chr1:225815800-225820000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:225815800-225823200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:225815800-225823400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:225815800-225823400	Weak transcription	Stomach Mucosa	stomach
27	chr1:225815800-225825400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:225815800-225839000	Weak transcription	Fetal Intestine Large	intestine
29	chr1:225816000-225825600	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:225816000-225825800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:225816000-225825800	Weak transcription	HepG2	liver
32	chr1:225816000-225830000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:225816000-225832400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:225816000-225834200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:225816000-225838400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:225816000-225838600	Weak transcription	Fetal Kidney	kidney
37	chr1:225816200-225823200	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:225816200-225835400	Weak transcription	Fetal Heart	heart
39	chr1:225816200-225836000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:225816200-225836600	Weak transcription	Adipose Nuclei	Adipose
41	chr1:225816800-225832000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:225817000-225820600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:225817000-225825400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:225817000-225825400	Weak transcription	Brain Germinal Matrix	brain
45	chr1:225817200-225819200	Enhancers	Rectal Smooth Muscle	rectum
46	chr1:225817200-225834000	Weak transcription	Psoas Muscle	Psoas
47	chr1:225817400-225819200	Enhancers	Colon Smooth Muscle	Colon
48	chr1:225817800-225819800	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr1:225818200-225819400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:225818400-225819200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links