Variant report

Variant	rs3799844
Chromosome Location	chr6:110022699-110022700
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1321329	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1406898	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1535419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17070657	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17070666	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17070692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17070701	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17070705	1.00[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[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17070733	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17070737	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17070740	1.00[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[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17070743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17070774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17070803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17070833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17070875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17070915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17070921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17070937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3778479	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3799848	1.00[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[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799850	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41439948	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4454171	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57181024	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57996937	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58273806	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58731181	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59203807	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59626863	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60108304	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60927725	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61374793	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61522207	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61671496	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9487130	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9487131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9487143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9791294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv933105	chr6:109933270-110064342	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv830769	chr6:109944334-110078120	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv604485	chr6:109959269-110054486	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110023600	Weak transcription	Gastric	stomach
2	chr6:110013000-110024800	Weak transcription	Lung	lung
3	chr6:110013000-110025200	Weak transcription	Small Intestine	intestine
4	chr6:110013000-110027400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:110013000-110027400	Weak transcription	Spleen	Spleen
6	chr6:110013000-110057000	Weak transcription	Left Ventricle	heart
7	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
8	chr6:110013200-110024200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:110013200-110026400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:110013200-110026600	Weak transcription	Ovary	ovary
11	chr6:110013200-110034000	Weak transcription	Fetal Stomach	stomach
12	chr6:110013200-110057000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:110013200-110057000	Weak transcription	Aorta	Aorta
14	chr6:110013400-110023200	Weak transcription	Fetal Intestine Large	intestine
15	chr6:110013400-110038600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:110013600-110056000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:110013600-110056800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:110013800-110026400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:110013800-110026600	Weak transcription	Brain Substantia Nigra	brain
20	chr6:110013800-110029600	Weak transcription	Fetal Lung	lung
21	chr6:110014000-110027400	Weak transcription	Brain Angular Gyrus	brain
22	chr6:110014000-110034400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:110014400-110023600	Weak transcription	Thymus	Thymus
24	chr6:110014600-110026600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:110014800-110023200	Weak transcription	Stomach Mucosa	stomach
26	chr6:110014800-110023600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:110014800-110023800	Weak transcription	Fetal Thymus	thymus
28	chr6:110014800-110026200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr6:110014800-110026400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:110014800-110026600	Weak transcription	Liver	Liver
31	chr6:110014800-110026800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr6:110014800-110027400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:110014800-110027400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:110014800-110034200	Weak transcription	Fetal Intestine Small	intestine
35	chr6:110015000-110026200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:110015000-110026200	Weak transcription	Brain Hippocampus Middle	brain
37	chr6:110017000-110023800	Weak transcription	Primary T cells from cord blood	blood
38	chr6:110017200-110024000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr6:110017600-110027000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:110017800-110023600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:110018000-110024800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:110018200-110024000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr6:110018200-110026600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:110018800-110034200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:110019000-110026600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:110020600-110027800	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr6:110022200-110022800	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr6:110022200-110022800	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr6:110022200-110024200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:110022200-110025000	Enhancers	HUES6 Cell Line	embryonic stem cell

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