Variant report

Variant	rs2973604
Chromosome Location	chr5:126148085-126148086
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	chr5:126145493..126147146-chr5:126147847..126149410,2	MCF-7	breast:
2	chr5:126112758..126116358-chr5:126145679..126148817,3	K562	blood:

Variant related genes	Relation type
ENSG00000113368	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10065951	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10478753	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1912570	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2136878	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2941661	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2941664	0.83[ASN][1000 genomes]
rs2941666	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2941673	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2973583	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2973587	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2973588	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2973589	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973596	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2973600	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2973886	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2973887	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973890	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4075655	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4267910	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62391702	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[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	nsv949054	chr5:125918148-126254480	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv534292	chr5:125993451-126259315	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 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	chr5:126114600-126161600	Weak transcription	Ovary	ovary
2	chr5:126130400-126165800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:126132200-126161200	Weak transcription	Gastric	stomach
4	chr5:126136000-126175200	Strong transcription	Dnd41	blood
5	chr5:126136400-126162400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:126137600-126154600	Weak transcription	Fetal Kidney	kidney
7	chr5:126137600-126166600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:126139800-126148200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:126139800-126160600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:126139800-126175400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:126140000-126150600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:126140000-126162000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:126140000-126162200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr5:126140000-126175200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:126140000-126175400	Strong transcription	Fetal Thymus	thymus
16	chr5:126140200-126150600	Strong transcription	Thymus	Thymus
17	chr5:126140200-126161400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr5:126140200-126161800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:126140200-126162600	Weak transcription	Colonic Mucosa	Colon
20	chr5:126140200-126163400	Weak transcription	Pancreas	Pancrea
21	chr5:126140400-126150000	Strong transcription	Fetal Muscle Leg	muscle
22	chr5:126140400-126150600	Strong transcription	Fetal Muscle Trunk	muscle
23	chr5:126140400-126161200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:126140400-126161800	Weak transcription	Placenta	Placenta
25	chr5:126140400-126162200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr5:126140600-126161600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr5:126140800-126161400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:126141000-126159200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:126141000-126177400	Weak transcription	Small Intestine	intestine
30	chr5:126141200-126161400	Weak transcription	Lung	lung
31	chr5:126141200-126181800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr5:126141400-126150400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:126141400-126174200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:126141600-126150600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:126141600-126150600	Strong transcription	Fetal Stomach	stomach
36	chr5:126141600-126162200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:126141600-126167400	Weak transcription	Brain Substantia Nigra	brain
38	chr5:126142000-126149200	Strong transcription	Hela-S3	cervix
39	chr5:126142600-126161200	Weak transcription	Spleen	Spleen
40	chr5:126142800-126157400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr5:126143600-126150000	Strong transcription	Fetal Intestine Small	intestine
42	chr5:126144200-126161600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr5:126144400-126173200	Weak transcription	Esophagus	oesophagus
44	chr5:126145000-126149600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
45	chr5:126145200-126153400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr5:126145400-126150200	Strong transcription	HepG2	liver
47	chr5:126145600-126148600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr5:126145600-126148600	Genic enhancers	Primary monocytes fromperipheralblood	blood
49	chr5:126145600-126152800	Strong transcription	HSMM	muscle
50	chr5:126145600-126153200	Strong transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links