Variant report

Variant	rs6846899
Chromosome Location	chr4:148762097-148762098
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	chr4:148761236..148763428-chr4:148766244..148769125,3	MCF-7	breast:
2	chr4:148671335..148673992-chr4:148761092..148763924,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10004850	0.93[EUR][1000 genomes]
rs10007231	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10018820	0.86[JPT][hapmap]
rs10018903	0.86[JPT][hapmap]
rs10021936	0.89[EUR][1000 genomes]
rs10022691	0.89[EUR][1000 genomes]
rs10023057	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10025684	0.89[EUR][1000 genomes]
rs10030513	0.89[EUR][1000 genomes]
rs1013842	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10461235	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs11099670	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724795	0.81[CHD][hapmap]
rs11733409	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11737346	0.92[CEU][hapmap];0.80[CHB][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs12498257	1.00[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12511313	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13129747	0.91[EUR][1000 genomes]
rs13148956	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13434396	0.89[EUR][1000 genomes]
rs1347596	0.84[EUR][1000 genomes]
rs1436489	1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1436490	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1469865	1.00[CEU][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1469867	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17023928	0.86[JPT][hapmap]
rs17023995	0.83[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs28662484	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35115631	0.91[EUR][1000 genomes]
rs4240338	0.85[CHD][hapmap];0.82[MEX][hapmap]
rs4240339	0.85[CHD][hapmap]
rs4240341	0.83[GIH][hapmap]
rs4835101	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4835461	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4835463	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4835464	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6535565	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6839440	0.88[EUR][1000 genomes]
rs6846526	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6853296	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71616571	0.85[EUR][1000 genomes]
rs7654433	1.00[CEU][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7655236	0.82[MEX][hapmap]
rs7664567	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7666127	0.86[JPT][hapmap]
rs893023	0.80[LWK][hapmap]
rs893024	1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9996108	0.85[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv880243	chr4:148735644-148879583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6846899	LSM6	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148737800-148782200	Weak transcription	Thymus	Thymus
2	chr4:148743200-148782200	Weak transcription	Fetal Intestine Large	intestine
3	chr4:148746400-148768000	Weak transcription	Fetal Intestine Small	intestine
4	chr4:148751400-148776000	Weak transcription	Fetal Stomach	stomach
5	chr4:148753200-148763600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:148753200-148765800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:148753200-148767800	Weak transcription	Small Intestine	intestine
8	chr4:148753400-148765800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:148753400-148782000	Weak transcription	Gastric	stomach
10	chr4:148754000-148766200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:148754400-148762200	Weak transcription	HUVEC	blood vessel
12	chr4:148754400-148769000	Weak transcription	NHLF	lung
13	chr4:148754600-148764000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:148754800-148763600	Weak transcription	HMEC	breast
15	chr4:148755200-148763000	Weak transcription	Left Ventricle	heart
16	chr4:148755200-148763200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:148755600-148773200	Weak transcription	Esophagus	oesophagus
18	chr4:148755800-148764000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:148756400-148766000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr4:148756400-148768000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:148756800-148763000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:148756800-148763000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr4:148756800-148766200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:148756800-148777800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:148757200-148763600	Weak transcription	NHDF-Ad	bronchial
26	chr4:148757400-148767400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:148757400-148767600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:148757600-148766200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:148757800-148763800	Weak transcription	HSMMtube	muscle
30	chr4:148758000-148763600	Weak transcription	HSMM	muscle
31	chr4:148759000-148762200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr4:148760400-148762600	Enhancers	Rectal Smooth Muscle	rectum
33	chr4:148760600-148763200	Enhancers	Ovary	ovary
34	chr4:148760800-148764600	Enhancers	Colon Smooth Muscle	Colon
35	chr4:148761000-148762400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:148761000-148764600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr4:148761000-148764600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr4:148761200-148762200	Genic enhancers	Aorta	Aorta
39	chr4:148761200-148763200	Enhancers	GM12878-XiMat	blood
40	chr4:148761200-148764200	Enhancers	Adipose Nuclei	Adipose
41	chr4:148761200-148764400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:148761200-148764800	Enhancers	Fetal Muscle Leg	muscle
43	chr4:148761400-148762200	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr4:148761400-148762200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:148761400-148762400	Enhancers	NH-A	brain
46	chr4:148761400-148764200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr4:148761400-148767800	Weak transcription	Fetal Kidney	kidney
48	chr4:148761600-148762400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:148761800-148762400	Enhancers	Right Ventricle	heart
50	chr4:148761800-148763200	Enhancers	Primary monocytes fromperipheralblood	blood

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