Variant report

Variant	rs6906460
Chromosome Location	chr6:25977361-25977362
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25974122..25975639-chr6:25976693..25979286,2	MCF-7	breast:
2	chr6:25975630..25979207-chr6:25990333..25993893,5	MCF-7	breast:
3	chr6:25971054..25973190-chr6:25974821..25978453,3	MCF-7	breast:
4	chr6:25972862..25974382-chr6:25976355..25979855,3	K562	blood:

Variant related genes	Relation type
ENSG00000272462	Chromatin interaction
ENSG00000272065	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10484431	1.00[JPT][hapmap]
rs10484434	0.90[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11751732	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11755492	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11756400	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11757088	1.00[JPT][hapmap]
rs11758372	1.00[JPT][hapmap]
rs11758378	0.83[EUR][1000 genomes]
rs11759668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11961143	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11964886	1.00[JPT][hapmap]
rs11965426	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11969868	1.00[JPT][hapmap]
rs16891142	1.00[JPT][hapmap]
rs17531978	1.00[JPT][hapmap]
rs17596719	1.00[JPT][hapmap]
rs185635	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs199729	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs199730	0.85[ASN][1000 genomes]
rs199738	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2051538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2071302	1.00[JPT][hapmap]
rs2230654	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34956419	0.81[ASN][1000 genomes]
rs36125084	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799374	0.81[ASN][1000 genomes]
rs41266783	0.85[EUR][1000 genomes]
rs412968	0.85[ASN][1000 genomes]
rs55661658	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56073264	0.81[ASN][1000 genomes]
rs59281021	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61289224	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62000984	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62394540	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62394542	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62394550	0.80[EUR][1000 genomes]
rs62394555	0.81[ASN][1000 genomes]
rs62394556	0.81[ASN][1000 genomes]
rs62396160	0.81[ASN][1000 genomes]
rs62396164	0.81[ASN][1000 genomes]
rs66505449	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66536062	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6925912	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935470	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7746105	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7757646	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7773526	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9689245	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	esv2755446	chr6:25924513-25981648	Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv432857	chr6:25957109-26072445	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	451 gene(s)	inside rSNPs	diseases
9	nsv1015627	chr6:25973495-26100483	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
10	nsv538164	chr6:25973495-26100483	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6906460	TRIM38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25964400-25981400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:25964800-25978800	Strong transcription	Fetal Thymus	thymus
3	chr6:25965000-25979200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr6:25965600-25985600	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:25967200-25977600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:25967200-25979200	Strong transcription	Thymus	Thymus
7	chr6:25967200-25981000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:25967200-25992000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:25967800-25992000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr6:25968400-25979600	Strong transcription	Stomach Smooth Muscle	stomach
11	chr6:25968400-25981200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:25968400-25985600	Strong transcription	Primary hematopoietic stem cells	blood
13	chr6:25968400-25987600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:25968600-25977600	Strong transcription	Ovary	ovary
15	chr6:25968600-25978800	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr6:25968600-25979200	Strong transcription	Fetal Muscle Leg	muscle
17	chr6:25968600-25986000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr6:25968600-25987200	Strong transcription	Duodenum Mucosa	Duodenum
19	chr6:25968800-25979200	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:25968800-25986600	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr6:25968800-25989400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr6:25969000-25986600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:25969000-25989600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr6:25969200-25979200	Strong transcription	Primary T cells from cord blood	blood
25	chr6:25969200-25989400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr6:25969400-25979200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:25970600-25979200	Strong transcription	Colon Smooth Muscle	Colon
28	chr6:25971000-25979800	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr6:25971400-25987200	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr6:25971400-25989400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:25971800-25979200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:25971800-25979400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:25972000-25979200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:25972000-25979200	Strong transcription	Spleen	Spleen
35	chr6:25972000-25979400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:25972000-25979800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:25972000-25979800	Strong transcription	Fetal Intestine Large	intestine
38	chr6:25972200-25978400	Strong transcription	Colonic Mucosa	Colon
39	chr6:25972200-25978800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr6:25972200-25979200	Strong transcription	Fetal Stomach	stomach
41	chr6:25972200-25979600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:25972200-25986000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:25972200-25987800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr6:25972200-25988600	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:25972400-25979200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:25972400-25979200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr6:25972400-25979400	Strong transcription	Adipose Nuclei	Adipose
48	chr6:25972400-25979400	Strong transcription	HSMMtube	muscle
49	chr6:25972400-25980600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:25972400-25985400	Strong transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links