Variant report

Variant	rs3800110
Chromosome Location	chr6:1874221-1874222
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10484694	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12192948	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13209589	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs13218267	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1570534	0.88[CEU][hapmap]
rs1977262	0.81[AFR][1000 genomes]
rs1980713	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap]
rs34660383	0.82[EUR][1000 genomes]
rs3778544	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3800116	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3800117	0.92[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3800119	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4959159	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4959616	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6930647	0.87[CEU][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes]
rs7776397	1.00[CEU][hapmap];0.91[YRI][hapmap];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	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
6	nsv538094	chr6:1757776-1907505	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv883383	chr6:1775436-1918572	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	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
11	nsv1019895	chr6:1832936-1882435	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	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
13	nsv883385	chr6:1869592-1915828	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1851200-1895600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:1851400-1909600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:1857600-1877200	Weak transcription	Primary T cells from cord blood	blood
4	chr6:1865200-1884600	Weak transcription	Small Intestine	intestine
5	chr6:1869400-1874400	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr6:1871000-1895400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:1871400-1876600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:1871600-1874400	Enhancers	Fetal Muscle Leg	muscle
9	chr6:1872000-1874400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:1872000-1874400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:1872000-1874400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:1872200-1874400	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr6:1872200-1874600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:1872400-1874400	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr6:1872600-1874400	Enhancers	Ovary	ovary
16	chr6:1872600-1874400	Enhancers	HSMM	muscle
17	chr6:1872600-1885800	Weak transcription	Gastric	stomach
18	chr6:1872800-1874400	Enhancers	Pancreas	Pancrea
19	chr6:1873200-1874400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:1873200-1874400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:1873200-1874400	Enhancers	Right Ventricle	heart
22	chr6:1873400-1874400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:1873400-1874400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:1873400-1885800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:1873600-1874400	Enhancers	HSMMtube	muscle
26	chr6:1873600-1874600	Flanking Active TSS	Brain Substantia Nigra	brain
27	chr6:1873600-1885600	Weak transcription	Fetal Intestine Small	intestine
28	chr6:1873800-1874400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:1873800-1874600	Strong transcription	HepG2	liver
30	chr6:1873800-1880400	Weak transcription	Aorta	Aorta
31	chr6:1873800-1885800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:1873800-1893000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:1874000-1874400	Active TSS	Brain Cingulate Gyrus	brain
34	chr6:1874000-1874400	Enhancers	Fetal Muscle Trunk	muscle
35	chr6:1874000-1874400	Enhancers	Psoas Muscle	Psoas
36	chr6:1874200-1874400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:1874200-1874400	Active TSS	Brain Anterior Caudate	brain
38	chr6:1874200-1874400	Active TSS	Brain Hippocampus Middle	brain
39	chr6:1874200-1874400	Bivalent Enhancer	Left Ventricle	heart
40	chr6:1874200-1881400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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