Variant report

Variant	rs2941673
Chromosome Location	chr5:126159441-126159442
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:126145438..126148189-chr5:126159181..126160876,2	K562	blood:
2	chr5:126159319..126160839-chr5:126161011..126162528,2	K562	blood:
3	chr5:126158979..126160898-chr5:126165536..126167471,2	MCF-7	breast:
4	chr5:126156930..126159583-chr5:126163283..126166232,2	K562	blood:
5	chr5:126145135..126148189-chr5:126159181..126162252,3	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	0.91[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10478753	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1912570	0.86[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2136878	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2941661	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2941664	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2941666	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2973583	0.95[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2973587	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2973588	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2973589	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2973596	0.96[CEU][hapmap];0.82[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2973600	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2973604	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2973886	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2973887	0.93[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2973890	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4075655	0.86[ASW][hapmap];0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4267910	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62391702	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[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:120 , 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	chr5:126137600-126166600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:126139800-126160600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:126139800-126175400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:126140000-126162000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:126140000-126162200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:126140000-126175200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:126140000-126175400	Strong transcription	Fetal Thymus	thymus
13	chr5:126140200-126161400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:126140200-126161800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:126140200-126162600	Weak transcription	Colonic Mucosa	Colon
16	chr5:126140200-126163400	Weak transcription	Pancreas	Pancrea
17	chr5:126140400-126161200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:126140400-126161800	Weak transcription	Placenta	Placenta
19	chr5:126140400-126162200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr5:126140600-126161600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr5:126140800-126161400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:126141000-126177400	Weak transcription	Small Intestine	intestine
23	chr5:126141200-126161400	Weak transcription	Lung	lung
24	chr5:126141200-126181800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr5:126141400-126174200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:126141600-126162200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:126141600-126167400	Weak transcription	Brain Substantia Nigra	brain
28	chr5:126142600-126161200	Weak transcription	Spleen	Spleen
29	chr5:126144200-126161600	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr5:126144400-126173200	Weak transcription	Esophagus	oesophagus
31	chr5:126146000-126183200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr5:126146000-126183600	Weak transcription	Left Ventricle	heart
33	chr5:126147400-126161600	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr5:126147600-126161600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr5:126147600-126167600	Strong transcription	GM12878-XiMat	blood
36	chr5:126147800-126161400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr5:126147800-126161800	Weak transcription	Brain Anterior Caudate	brain
38	chr5:126147800-126165600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr5:126147800-126170400	Weak transcription	Stomach Mucosa	stomach
40	chr5:126147800-126171600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:126148200-126161400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr5:126148200-126161400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr5:126148200-126162200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr5:126148200-126182400	Weak transcription	HSMMtube	muscle
45	chr5:126148200-126193200	Weak transcription	Brain Angular Gyrus	brain
46	chr5:126149200-126170000	Weak transcription	Aorta	Aorta
47	chr5:126149600-126181400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr5:126150800-126161000	Weak transcription	NHLF	lung
49	chr5:126151200-126161800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:126151200-126162600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links