Variant report

Variant	rs3800136
Chromosome Location	chr6:1921848-1921849
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1918511..1920955-chr6:1921418..1923384,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10900914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11969985	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12524972	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12528819	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12530211	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664587	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1570535	0.86[JPT][hapmap]
rs1570537	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17134549	0.81[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17134557	0.81[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2281760	0.86[JPT][hapmap]
rs2628442	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2628443	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2628445	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2628455	0.87[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2761233	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2761235	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3800121	0.86[JPT][hapmap]
rs4512269	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4959160	0.86[JPT][hapmap]
rs56031192	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56226194	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62390680	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62390682	0.80[EUR][1000 genomes]
rs62391624	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62391626	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62391627	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62391628	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62391632	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6914444	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6916130	0.93[CHB][hapmap];0.92[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72841994	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7759192	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7759496	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs912310	0.86[JPT][hapmap]

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	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
6	nsv883384	chr6:1787862-1942538	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1032149	chr6:1848148-2006021	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1032727	chr6:1900622-2064690	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv538095	chr6:1900622-2064690	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv883386	chr6:1910108-2122454	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3800136	LYRM4	cis	parietal	SCAN
rs3800136	NEFH	trans	lymphoblastoid	seeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1901600-1923400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:1905000-1970600	Weak transcription	Spleen	Spleen
3	chr6:1905200-1926000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:1905200-1926000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:1905400-1962000	Weak transcription	Pancreas	Pancrea
6	chr6:1908400-1933600	Weak transcription	Liver	Liver
7	chr6:1909800-1926000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:1910200-1965800	Weak transcription	Small Intestine	intestine
9	chr6:1914800-1930800	Strong transcription	HepG2	liver
10	chr6:1915200-1934000	Weak transcription	Left Ventricle	heart
11	chr6:1915200-1937600	Weak transcription	Esophagus	oesophagus
12	chr6:1915800-1923400	Weak transcription	Fetal Intestine Large	intestine
13	chr6:1915800-1923400	Weak transcription	Fetal Stomach	stomach
14	chr6:1915800-1972800	Weak transcription	Colonic Mucosa	Colon
15	chr6:1916000-1928600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:1916000-1960800	Weak transcription	Gastric	stomach
17	chr6:1916200-1930000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:1916600-1926200	Weak transcription	Fetal Intestine Small	intestine
19	chr6:1916600-1935000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:1917000-1926000	Weak transcription	Thymus	Thymus
21	chr6:1917400-1923600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:1918000-1933600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:1918200-1923200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:1918200-1923600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:1918200-1925800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:1918200-1926400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:1918200-1927600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:1918200-1930200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:1918600-1927800	Weak transcription	Hela-S3	cervix
30	chr6:1918600-1929400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:1918600-1933400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:1918600-1946400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:1918600-1957800	Weak transcription	Dnd41	blood
34	chr6:1918800-1930800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:1919000-1928800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr6:1919000-1930200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:1919000-1933000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr6:1919200-1934400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:1919400-1930200	Weak transcription	Aorta	Aorta
40	chr6:1919600-1962400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr6:1920200-1932000	Weak transcription	Primary B cells from cord blood	blood
42	chr6:1920400-1925800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr6:1920400-1925800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr6:1920400-1933200	Weak transcription	GM12878-XiMat	blood
45	chr6:1920800-1922400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:1920800-1922600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:1920800-1926200	Weak transcription	Primary T cells from cord blood	blood
48	chr6:1921400-1926200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr6:1921600-1931000	Weak transcription	Fetal Kidney	kidney

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