Variant report

Variant	rs1175627
Chromosome Location	chr1:112959614-112959615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:112954892..112957372-chr1:112957566..112961272,3	MCF-7	breast:
2	chr1:112951394..112954161-chr1:112958063..112960913,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143079	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1175624	0.87[AFR][1000 genomes]
rs1175628	0.87[AFR][1000 genomes]
rs1175637	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1175639	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175640	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1175642	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1175643	0.87[AFR][1000 genomes]
rs1175644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175647	0.82[AFR][1000 genomes]
rs1759691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1777621	0.87[AFR][1000 genomes]
rs2483347	0.87[AFR][1000 genomes]
rs2780274	0.92[AFR][1000 genomes]
rs2780276	1.00[YRI][hapmap];0.87[AFR][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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers 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	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1850997	chr1:112944472-112993754	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112940000-112961400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:112940600-112962000	Weak transcription	Psoas Muscle	Psoas
3	chr1:112942400-112988200	Weak transcription	Small Intestine	intestine
4	chr1:112942600-112966400	Weak transcription	Spleen	Spleen
5	chr1:112942600-112967000	Weak transcription	Pancreas	Pancrea
6	chr1:112945000-112966400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:112946800-112960800	Weak transcription	Brain Substantia Nigra	brain
8	chr1:112946800-112970600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:112947200-112961800	Weak transcription	A549	lung
10	chr1:112947200-112961800	Weak transcription	HepG2	liver
11	chr1:112947200-112971200	Weak transcription	Aorta	Aorta
12	chr1:112947200-112981000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:112947400-112965600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:112949200-112960600	Weak transcription	Brain Angular Gyrus	brain
15	chr1:112949200-112963200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:112949200-112966400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:112950000-112960000	Weak transcription	Fetal Lung	lung
18	chr1:112951200-112969000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:112951600-112968800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:112952000-112969600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:112952400-112960800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:112952400-112990600	Weak transcription	Esophagus	oesophagus
23	chr1:112952600-112963400	Weak transcription	Stomach Mucosa	stomach
24	chr1:112952600-112981400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:112953800-112966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:112954400-112959800	Weak transcription	Gastric	stomach
27	chr1:112954400-112960200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:112954400-112960200	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr1:112954400-112960400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:112954400-112962600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:112954400-112962600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:112954400-112962600	Strong transcription	HUVEC	blood vessel
33	chr1:112954400-112963200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:112954400-112963400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:112954400-112963800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:112954400-112964000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:112954400-112964600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:112954400-112967400	Strong transcription	Osteobl	bone
39	chr1:112954600-112960000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:112954600-112960200	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr1:112954600-112960600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:112954600-112961600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:112954600-112961800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:112954600-112962000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:112954600-112962200	Strong transcription	NH-A	brain
46	chr1:112954600-112962800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:112954800-112960600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:112954800-112961400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:112954800-112962600	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:112955000-112960600	Strong transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links