Variant report

Variant	rs2219667
Chromosome Location	chr6:106994326-106994327
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:106958366..106960246-chr6:106994046..106995660,2	MCF-7	breast:
2	chr6:106982665..106985601-chr6:106993025..106995759,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112297	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11759221	0.82[ASN][1000 genomes]
rs11968064	0.90[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs12523774	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs12526141	0.90[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1419054	0.88[JPT][hapmap]
rs1462147	0.90[CHB][hapmap]
rs17052215	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2066202	0.84[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2126395	0.91[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2247346	0.90[CHB][hapmap]
rs3747790	0.88[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs4946763	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57424436	0.82[ASN][1000 genomes]
rs58972320	0.82[ASN][1000 genomes]
rs6935354	0.91[CEU][hapmap]
rs7738230	0.90[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs9386567	0.81[ASN][1000 genomes]
rs9480687	0.81[ASN][1000 genomes]
rs9486406	0.81[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2219667	SCML4	cis	parietal	SCAN
rs2219667	QRSL1	cis	parietal	SCAN

Chromatin state (count:82 , 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	chr6:106981600-106995600	Weak transcription	Colonic Mucosa	Colon
6	chr6:106982400-107000800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:106985800-107019200	Weak transcription	Aorta	Aorta
8	chr6:106986400-106994600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:106986400-106995000	Weak transcription	Thymus	Thymus
10	chr6:106986800-106994400	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr6:106988200-107001400	Weak transcription	Lung	lung
12	chr6:106988400-106995600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:106988800-106994600	Strong transcription	Duodenum Mucosa	Duodenum
14	chr6:106989200-106994600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:106989800-106995800	Weak transcription	Fetal Stomach	stomach
16	chr6:106991200-106994600	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr6:106991200-106999600	Strong transcription	Dnd41	blood
18	chr6:106991400-106994800	Strong transcription	Liver	Liver
19	chr6:106992000-106994800	Weak transcription	Fetal Intestine Small	intestine
20	chr6:106992000-106995400	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:106992600-106996400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:106992600-106996600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:106992800-106994400	Genic enhancers	Primary B cells from cord blood	blood
24	chr6:106992800-106995800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:106993000-106994400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:106993200-106994400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:106993200-106994400	Enhancers	HUVEC	blood vessel
28	chr6:106993200-106994400	Genic enhancers	NHEK	skin
29	chr6:106993200-106994600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr6:106993200-106996400	Genic enhancers	Primary B cells from peripheral blood	blood
31	chr6:106993200-106996600	Enhancers	Primary hematopoietic stem cells	blood
32	chr6:106993400-106994400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:106993400-106994600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:106993400-106995000	Genic enhancers	Placenta	Placenta
35	chr6:106993400-106995200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:106993400-106996000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
37	chr6:106993400-106996000	Enhancers	Adipose Nuclei	Adipose
38	chr6:106993600-106994400	Weak transcription	Fetal Thymus	thymus
39	chr6:106993600-106994600	Enhancers	Fetal Muscle Leg	muscle
40	chr6:106993600-106996200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:106993600-106998400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr6:106993800-106994400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
43	chr6:106993800-106994600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:106993800-106994600	Enhancers	Spleen	Spleen
45	chr6:106993800-106994800	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr6:106993800-106995000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr6:106993800-106995000	Enhancers	NHLF	lung
48	chr6:106993800-106995800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
49	chr6:106993800-106996200	Enhancers	HSMM	muscle
50	chr6:106993800-106996400	Enhancers	Fetal Lung	lung

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