Variant report

Variant	rs11758378
Chromosome Location	chr6:26047484-26047485
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr6:26047302-26047497	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr6:26047082-26047556	MCF-7	breast:	n/a	chr6:26047332-26047340
3	GATA3	chr6:26047124-26047509	MCF-7	breast:	n/a	chr6:26047332-26047340
4	STAT3	chr6:26047137-26047519	MCF10A-Er-Src	breast:	n/a	chr6:26047351-26047362
5	STAT3	chr6:26047139-26047527	MCF10A-Er-Src	breast:	n/a	chr6:26047351-26047362
6	STAT3	chr6:26047105-26047526	MCF10A-Er-Src	breast:	n/a	chr6:26047351-26047362
7	GATA3	chr6:26046999-26047506	SK-N-SH	brain:	n/a	chr6:26047332-26047340
8	HA-E2F1	chr6:26047238-26047771	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:26044671..26047980-chr6:26183838..26186075,3	MCF-7	breast:
2	chr17:56708294..56710638-chr6:26044705..26047582,3	MCF-7	breast:
3	chr6:26045666..26048095-chr6:26203965..26208002,5	MCF-7	breast:
4	chr6:26044526..26047786-chr6:27838310..27841317,7	MCF-7	breast:
5	chr6:26041051..26050922-chr6:26154916..26161227,19	MCF-7	breast:
6	chr6:26043872..26047495-chr6:26122651..26127553,11	MCF-7	breast:
7	chr6:26043570..26047536-chr6:26215421..26218540,6	MCF-7	breast:

Variant related genes	Relation type
HIST1H2BB	TF binding region
ENSG00000198558	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000182572	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000197697	Chromatin interaction
ENSG00000187990	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10484434	0.97[EUR][1000 genomes]
rs11751732	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11755492	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11756400	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11759668	0.89[EUR][1000 genomes]
rs11961143	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11965426	0.89[EUR][1000 genomes]
rs2051538	0.88[EUR][1000 genomes]
rs2230654	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34956419	0.87[ASN][1000 genomes]
rs36125084	0.83[EUR][1000 genomes]
rs3799374	0.87[ASN][1000 genomes]
rs41266783	0.97[EUR][1000 genomes]
rs55661658	0.85[EUR][1000 genomes]
rs56073264	0.87[ASN][1000 genomes]
rs59281021	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61289224	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62000984	0.95[EUR][1000 genomes]
rs62394540	0.87[EUR][1000 genomes]
rs62394542	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62394550	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62394555	0.87[ASN][1000 genomes]
rs62394556	0.87[ASN][1000 genomes]
rs62396160	0.87[ASN][1000 genomes]
rs62396164	0.87[ASN][1000 genomes]
rs66505449	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66536062	0.89[EUR][1000 genomes]
rs6906460	0.83[EUR][1000 genomes]
rs6925912	0.83[EUR][1000 genomes]
rs6935470	0.88[EUR][1000 genomes]
rs7757646	0.87[ASN][1000 genomes]
rs9689245	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
8	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
9	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
10	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
11	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
12	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
13	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
14	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
15	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
16	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
17	nsv1025493	chr6:26026870-26223838	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1001 gene(s)	inside rSNPs	diseases
18	nsv1023979	chr6:26026870-26287399	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1113 gene(s)	inside rSNPs	diseases
19	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
20	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
21	nsv1026692	chr6:26027408-26067081	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	363 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11758378	TRIM38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26034400-26048200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:26044600-26054800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:26044600-26055000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:26045800-26054600	Weak transcription	Ovary	ovary
5	chr6:26046000-26047800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:26046200-26048000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:26046200-26051000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:26046200-26054200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:26046200-26054600	Weak transcription	Esophagus	oesophagus
10	chr6:26046400-26048200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:26046400-26054200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:26046400-26054200	Weak transcription	Brain Angular Gyrus	brain
13	chr6:26046600-26047600	Weak transcription	Placenta	Placenta
14	chr6:26046600-26047800	Enhancers	NHEK	skin
15	chr6:26046600-26048000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:26046600-26048000	Enhancers	Hela-S3	cervix
17	chr6:26046600-26048200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:26046600-26048400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:26046600-26048400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:26046600-26048800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:26046600-26048800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:26046600-26049000	Weak transcription	Liver	Liver
23	chr6:26046600-26049400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr6:26046600-26049800	Enhancers	Dnd41	blood
25	chr6:26046600-26050600	Weak transcription	Thymus	Thymus
26	chr6:26046600-26051800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:26046600-26052000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr6:26046600-26052000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr6:26046600-26052400	Weak transcription	Stomach Mucosa	stomach
30	chr6:26046600-26052800	Weak transcription	Fetal Thymus	thymus
31	chr6:26046600-26054000	Weak transcription	Osteobl	bone
32	chr6:26046600-26054200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:26046600-26054200	Weak transcription	Fetal Kidney	kidney
34	chr6:26046600-26054200	Weak transcription	NHDF-Ad	bronchial
35	chr6:26046600-26054200	Weak transcription	NHLF	lung
36	chr6:26046800-26048400	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr6:26046800-26048400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:26046800-26049000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr6:26046800-26049600	Enhancers	A549	lung
40	chr6:26046800-26053600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr6:26046800-26053800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:26046800-26054400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr6:26047200-26054200	Weak transcription	HepG2	liver
44	chr6:26047400-26049800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:26047400-26052000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links