Variant report

Variant	rs6902745
Chromosome Location	chr6:106996372-106996373
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	chr6:106988236..106991971-chr6:106994585..106996382,3	MCF-7	breast:
2	chr6:106937771..106940207-chr6:106996030..106997572,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112297	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1111830	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1613722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616375	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1676008	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1676010	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1676023	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1676024	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1676025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1676026	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs1676028	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17067603	1.00[JPT][hapmap]
rs17565194	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1770718	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1770719	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1770720	0.91[CEU][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs1770721	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1770722	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1770723	1.00[ASN][1000 genomes]
rs1770733	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2066201	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2247335	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2615209	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747789	1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3804344	1.00[JPT][hapmap]
rs4945756	0.87[AFR][1000 genomes]
rs4946762	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs6911321	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs72945076	0.89[ASN][1000 genomes]
rs7771502	0.96[ASN][1000 genomes]
rs783395	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs783396	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs783401	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs783414	1.00[CHB][hapmap]
rs9386565	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9386566	0.87[AFR][1000 genomes]

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	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1017419	chr6:106984669-106997000	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6902745	QRSL1	cis	parietal	SCAN
rs6902745	QRSL1	cis	cerebellum	SCAN
rs6902745	SCML4	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106961000-107001400	Weak transcription	Gastric	stomach
2	chr6:106964800-107029800	Weak transcription	Small Intestine	intestine
3	chr6:106970600-107022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:106979000-107001400	Weak transcription	Pancreas	Pancrea
5	chr6:106982400-107000800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:106985800-107019200	Weak transcription	Aorta	Aorta
7	chr6:106988200-107001400	Weak transcription	Lung	lung
8	chr6:106991200-106999600	Strong transcription	Dnd41	blood
9	chr6:106992600-106996400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:106992600-106996600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:106993200-106996400	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr6:106993200-106996600	Enhancers	Primary hematopoietic stem cells	blood
13	chr6:106993600-106998400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr6:106993800-106996400	Enhancers	Fetal Lung	lung
15	chr6:106993800-106996400	Enhancers	Osteobl	bone
16	chr6:106993800-106996600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:106993800-106996600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr6:106993800-106996600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:106993800-106996600	Enhancers	NH-A	brain
20	chr6:106994000-106996600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:106994000-106996600	Enhancers	HepG2	liver
22	chr6:106994000-107017800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:106994200-106996400	Enhancers	A549	lung
24	chr6:106994200-106997000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:106994200-107000200	Weak transcription	Esophagus	oesophagus
26	chr6:106994200-107009000	Weak transcription	Left Ventricle	heart
27	chr6:106994200-107019400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:106994200-107019600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr6:106994400-106996600	Enhancers	Fetal Thymus	thymus
30	chr6:106994400-107000800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr6:106994600-106996400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:106994600-106996400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:106994600-106996600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:106994600-106996600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr6:106994600-106996600	Enhancers	Fetal Intestine Large	intestine
36	chr6:106994600-106996600	Enhancers	NHDF-Ad	bronchial
37	chr6:106994600-106997000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:106994600-106999600	Strong transcription	GM12878-XiMat	blood
39	chr6:106994600-107001400	Weak transcription	Spleen	Spleen
40	chr6:106994800-106996600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:106994800-106996600	Enhancers	Fetal Intestine Small	intestine
42	chr6:106994800-107000800	Weak transcription	Liver	Liver
43	chr6:106994800-107004200	Strong transcription	Primary T cells from cord blood	blood
44	chr6:106994800-107004600	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr6:106994800-107004600	Weak transcription	Hela-S3	cervix
46	chr6:106995000-106996600	Enhancers	HUVEC	blood vessel
47	chr6:106995000-106996600	Flanking Active TSS	NHEK	skin
48	chr6:106995000-106999200	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr6:106995000-106999200	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:106995000-107019400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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