Variant report

Variant	rs2143076
Chromosome Location	chr6:149746451-149746452
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149379361..149382289-chr6:149745014..149748004,4	MCF-7	breast:
2	chr6:149745176..149748304-chr6:149748732..149751749,4	MCF-7	breast:
3	chr6:149740980..149743677-chr6:149744800..149747765,2	K562	blood:
4	chr6:149744819..149747181-chr6:149748180..149751163,2	MCF-7	breast:
5	chr6:149352125..149354322-chr6:149744702..149746498,2	MCF-7	breast:
6	chr6:149348466..149350718-chr6:149745093..149747617,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236591	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs2179367	0.92[EUR][1000 genomes]
rs2262617	0.89[EUR][1000 genomes]
rs2341783	0.87[JPT][hapmap]
rs2341784	0.87[JPT][hapmap]
rs2744427	0.87[JPT][hapmap]
rs2744432	0.80[AMR][1000 genomes]
rs2744434	0.87[JPT][hapmap]
rs2789488	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2789490	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2789492	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789500	0.87[JPT][hapmap]
rs3734296	0.87[JPT][hapmap]
rs472810	0.86[JPT][hapmap]
rs474369	0.87[JPT][hapmap]
rs478767	0.87[JPT][hapmap]
rs480526	0.87[JPT][hapmap]
rs489551	0.85[ASN][1000 genomes]
rs4895788	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895789	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs4897124	0.89[EUR][1000 genomes]
rs4897125	0.87[EUR][1000 genomes]
rs492956	0.86[JPT][hapmap]
rs494340	0.82[JPT][hapmap]
rs501926	0.87[JPT][hapmap]
rs504762	0.83[JPT][hapmap]
rs504985	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs506268	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs511100	0.82[ASN][1000 genomes]
rs511105	0.87[JPT][hapmap]
rs514839	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs515133	0.83[JPT][hapmap]
rs521845	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs532250	0.83[JPT][hapmap]
rs536203	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs537354	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs538386	0.87[JPT][hapmap]
rs540538	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs544947	0.85[ASN][1000 genomes]
rs556335	0.87[JPT][hapmap]
rs559052	0.86[JPT][hapmap]
rs560051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs562428	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs564961	0.85[ASN][1000 genomes]
rs565825	0.86[JPT][hapmap]
rs570442	0.83[JPT][hapmap]
rs577001	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs579789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs580011	0.85[ASN][1000 genomes]
rs585022	0.81[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs600739	0.81[JPT][hapmap]
rs628488	0.85[ASN][1000 genomes]
rs638407	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs652807	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs652921	0.87[JPT][hapmap]
rs6570965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs663625	0.87[JPT][hapmap]
rs909793	0.81[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs9285519	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9322178	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9373589	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9373592	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9377212	0.85[ASN][1000 genomes]
rs9377218	0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs9390676	0.86[JPT][hapmap]
rs9390677	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9404034	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522875	chr6:149643709-149762537	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv517606	chr6:149744632-149755695	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv470866	chr6:149744632-149806552	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149709600-149750200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:149744000-149746800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:149745200-149746800	Enhancers	Placenta	Placenta
4	chr6:149745400-149746800	Weak transcription	Fetal Heart	heart
5	chr6:149745400-149748600	Weak transcription	HSMMtube	muscle
6	chr6:149745400-149750400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:149745600-149746600	Enhancers	Brain Cingulate Gyrus	brain
8	chr6:149745600-149746600	Enhancers	Brain Hippocampus Middle	brain
9	chr6:149745600-149747000	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr6:149745600-149749000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:149745600-149750200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:149745600-149752800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:149745600-149752800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:149745600-149752800	Weak transcription	HSMM	muscle
15	chr6:149745600-149753000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:149745600-149753000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:149745600-149753000	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:149746200-149746800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:149746400-149746800	Bivalent Enhancer	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links