Variant report

Variant	rs2970559
Chromosome Location	chr1:209380800-209380801
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209249394..209250232-chr1:209380730..209381661,2	MCF-7	breast:
2	chr1:209379971..209382311-chr1:209606603..209608628,2	MCF-7	breast:
3	chr1:209380711..209382110-chr1:209421741..209422984,5	MCF-7	breast:
4	chr1:208825434..208826290-chr1:209380727..209381616,2	MCF-7	breast:
5	chr1:209249788..209250661-chr1:209380684..209381520,2	MCF-7	breast:

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1395754	1.00[EUR][1000 genomes]
rs2174778	1.00[EUR][1000 genomes]
rs2843174	1.00[EUR][1000 genomes]
rs2843175	1.00[EUR][1000 genomes]
rs2843176	1.00[EUR][1000 genomes]
rs74155435	1.00[EUR][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	nsv832481	chr1:209371276-209540333	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209370400-209380800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209373200-209380800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:209373200-209381200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:209377000-209380800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:209377200-209381200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:209377400-209380800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:209380000-209380800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
8	chr1:209380200-209380800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:209380200-209380800	Enhancers	Fetal Brain Male	brain
10	chr1:209380200-209380800	Enhancers	Fetal Brain Female	brain
11	chr1:209380200-209381200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
12	chr1:209380400-209380800	Enhancers	Brain Germinal Matrix	brain
13	chr1:209380400-209380800	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr1:209380400-209380800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr1:209380400-209380800	Enhancers	Ovary	ovary
16	chr1:209380400-209380800	Bivalent Enhancer	Right Ventricle	heart
17	chr1:209380400-209381000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:209380400-209381200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:209380400-209381400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:209380400-209381400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:209380400-209381800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:209380600-209380800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
23	chr1:209380600-209380800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr1:209380600-209380800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
25	chr1:209380600-209380800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:209380600-209380800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:209380600-209380800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:209380600-209380800	Enhancers	Liver	Liver
29	chr1:209380600-209380800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:209380600-209380800	Enhancers	Colon Smooth Muscle	Colon
31	chr1:209380600-209380800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
32	chr1:209380600-209380800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
33	chr1:209380600-209380800	Bivalent Enhancer	Fetal Kidney	kidney
34	chr1:209380600-209380800	Enhancers	Fetal Lung	lung
35	chr1:209380600-209380800	Bivalent Enhancer	Fetal Muscle Leg	muscle
36	chr1:209380600-209380800	Bivalent/Poised TSS	Hela-S3	cervix
37	chr1:209380600-209380800	Enhancers	HMEC	breast
38	chr1:209380600-209380800	Enhancers	HSMM	muscle
39	chr1:209380600-209380800	Enhancers	NH-A	brain
40	chr1:209380600-209381000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
41	chr1:209380600-209381000	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:209380600-209381000	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr1:209380600-209381000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:209380600-209381000	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr1:209380600-209381000	Flanking Active TSS	Brain Cingulate Gyrus	brain
46	chr1:209380600-209381000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
47	chr1:209380600-209381000	Bivalent Enhancer	Fetal Stomach	stomach
48	chr1:209380600-209381000	Enhancers	Spleen	Spleen
49	chr1:209380600-209381200	Enhancers	H9 Cell Line	embryonic stem cell
50	chr1:209380600-209381200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links