Variant report

Variant	rs2677795
Chromosome Location	chr4:16029642-16029643
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:16026900..16029773-chr4:16034427..16036480,2	MCF-7	breast:
2	chr4:16028228..16030033-chr4:16225456..16227721,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169762	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs884718	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][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	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv916742	chr4:15797994-16064232	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2677795	PROM1	cis	Artery Aorta	GTEx
rs2677795	PROM1	cis	Artery Tibial	GTEx
rs2677795	PROM1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15964600-16031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:15988400-16033800	Weak transcription	Pancreas	Pancrea
3	chr4:16007000-16030800	Weak transcription	Fetal Kidney	kidney
4	chr4:16008000-16033000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:16009200-16033200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr4:16010800-16038600	Weak transcription	Placenta	Placenta
7	chr4:16013400-16030800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:16015400-16031200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:16018200-16030800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:16020600-16031000	Weak transcription	Gastric	stomach
11	chr4:16023600-16032400	Weak transcription	Fetal Brain Male	brain
12	chr4:16023600-16033600	Weak transcription	Fetal Brain Female	brain
13	chr4:16025200-16030400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:16025600-16030800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:16025600-16033800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:16025600-16035600	Weak transcription	Fetal Intestine Small	intestine
17	chr4:16025600-16045000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:16025600-16050600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:16025800-16030800	Weak transcription	Fetal Stomach	stomach
20	chr4:16025800-16031000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:16025800-16036000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr4:16025800-16057600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:16026200-16031000	Weak transcription	Fetal Muscle Leg	muscle
24	chr4:16026400-16030600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:16026400-16030600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:16026400-16030800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr4:16026400-16066600	Weak transcription	Colonic Mucosa	Colon
28	chr4:16026400-16066600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr4:16026600-16031000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:16027000-16030200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr4:16027000-16030400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:16027000-16034000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:16027200-16030600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:16027200-16030600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr4:16027200-16030800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:16027200-16039000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr4:16027400-16030800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr4:16027600-16036000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr4:16027800-16030200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:16028000-16030800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:16028000-16030800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:16028200-16031200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:16028400-16030800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:16028400-16030800	Weak transcription	Fetal Heart	heart
45	chr4:16028400-16033800	Weak transcription	Brain Angular Gyrus	brain
46	chr4:16028600-16030800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr4:16028600-16033200	Weak transcription	Brain Hippocampus Middle	brain
48	chr4:16029200-16030600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:16029200-16030800	Weak transcription	Aorta	Aorta
50	chr4:16029200-16031000	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links