Variant report

Variant	rs6438660
Chromosome Location	chr3:121493856-121493857
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	chr3:121469877..121471972-chr3:121492602..121496614,3	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10934560	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12489511	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12490565	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12631824	0.80[EUR][1000 genomes]
rs13067629	0.95[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap]
rs1492177	0.90[CEU][hapmap];0.83[CHB][hapmap]
rs1574655	0.83[EUR][1000 genomes]
rs1574735	0.83[EUR][1000 genomes]
rs17849995	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1873645	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs1919552	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs1919557	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs2001390	0.83[EUR][1000 genomes]
rs2001391	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs2070179	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs2141614	0.90[JPT][hapmap]
rs2332056	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2840143	0.90[CEU][hapmap];0.83[CHB][hapmap]
rs34920680	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34980632	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35713885	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36022362	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676689	0.81[EUR][1000 genomes]
rs4676690	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4676751	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4676754	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57420306	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59740137	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438661	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6770719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6771716	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6774164	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776703	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6777997	0.85[AFR][1000 genomes]
rs6791510	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6794341	0.83[EUR][1000 genomes]
rs6802033	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs6803839	0.95[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs6807711	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs73179983	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7375038	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs7429247	0.86[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs7611913	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs7646346	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7646585	0.95[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs9289172	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs9289173	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs9681049	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9681209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809114	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs9812411	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs9829053	0.84[EUR][1000 genomes]
rs9832267	0.81[EUR][1000 genomes]
rs9835182	0.83[EUR][1000 genomes]
rs9854052	0.81[EUR][1000 genomes]
rs9861992	0.80[EUR][1000 genomes]
rs9864907	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs9876021	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv432483	chr3:121488995-121629634	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv933820	chr3:121489302-121500759	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv934077	chr3:121491540-121507705	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv933987	chr3:121491698-121500759	Strong transcription Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv933526	chr3:121491698-121500853	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv932985	chr3:121491698-121507705	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6438660	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs6438660	HCLS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121477200-121494000	Weak transcription	Right Ventricle	heart
2	chr3:121478000-121499400	Weak transcription	HepG2	liver
3	chr3:121483600-121498600	Weak transcription	Fetal Kidney	kidney
4	chr3:121483800-121498400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:121484400-121494000	Weak transcription	Brain Angular Gyrus	brain
6	chr3:121484600-121499000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:121485600-121497200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:121485600-121503200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:121485800-121501000	Strong transcription	Duodenum Mucosa	Duodenum
10	chr3:121486200-121526600	Weak transcription	Stomach Mucosa	stomach
11	chr3:121486800-121496000	Weak transcription	Hela-S3	cervix
12	chr3:121486800-121532200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:121487000-121494000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:121487000-121498800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:121487000-121509000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:121487200-121501600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:121487400-121494200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:121487400-121494800	Strong transcription	HSMM	muscle
19	chr3:121487400-121495200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:121487400-121497200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:121487400-121499200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:121487400-121501400	Strong transcription	Primary T cells from cord blood	blood
23	chr3:121487400-121501400	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:121487400-121502000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:121487400-121503000	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:121487400-121512200	Strong transcription	Fetal Thymus	thymus
27	chr3:121487400-121512400	Strong transcription	Dnd41	blood
28	chr3:121487600-121495600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:121487600-121497200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:121487600-121498800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:121487800-121497600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:121487800-121509000	Strong transcription	Fetal Intestine Large	intestine
33	chr3:121487800-121516400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:121487800-121519000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr3:121488000-121507200	Weak transcription	Brain Substantia Nigra	brain
36	chr3:121488000-121511000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr3:121488000-121512200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:121488000-121512600	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:121488200-121501800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:121488400-121505600	Weak transcription	Fetal Heart	heart
41	chr3:121488400-121509600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:121488600-121494200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:121488600-121501000	Strong transcription	Liver	Liver
44	chr3:121488600-121502000	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:121488600-121509000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:121488600-121510200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr3:121488600-121517800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr3:121488800-121494000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:121488800-121494200	Strong transcription	Brain Hippocampus Middle	brain
50	chr3:121488800-121494200	Strong transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links