Variant report

Variant	rs1890543
Chromosome Location	chr6:128712447-128712448
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1416518	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17055834	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2326682	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4351279	0.82[YRI][hapmap];0.92[AFR][1000 genomes]
rs4895834	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57524201	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6569526	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73589563	0.88[AFR][1000 genomes]
rs73589574	0.86[AFR][1000 genomes]
rs73589577	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7754771	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7758826	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs8180639	0.87[YRI][hapmap];0.92[AFR][1000 genomes]
rs9388633	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs946425	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs946426	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS 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	15 gene(s)	inside rSNPs	diseases
5	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128679600-128732000	Weak transcription	Left Ventricle	heart
2	chr6:128688800-128738800	Weak transcription	Psoas Muscle	Psoas
3	chr6:128691600-128730400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr6:128697800-128733400	Weak transcription	HSMM	muscle
5	chr6:128698800-128724000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:128698800-128743200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:128699200-128715000	Weak transcription	HepG2	liver
8	chr6:128699600-128720400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:128699600-128724000	Weak transcription	NHEK	skin
10	chr6:128701800-128725400	Weak transcription	Ovary	ovary
11	chr6:128702200-128716200	Weak transcription	Liver	Liver
12	chr6:128703200-128716400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:128703200-128743000	Weak transcription	Pancreas	Pancrea
14	chr6:128704400-128715400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:128706800-128731800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:128707800-128720800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:128708800-128712800	Enhancers	Fetal Heart	heart
18	chr6:128710200-128717800	Weak transcription	Fetal Intestine Small	intestine
19	chr6:128710200-128729800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:128710200-128739800	Weak transcription	Fetal Intestine Large	intestine
21	chr6:128711200-128714600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:128711200-128726800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:128711400-128715000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:128711600-128715000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:128711600-128715600	Weak transcription	Fetal Lung	lung
26	chr6:128711600-128716400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:128711600-128721800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:128711800-128715400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:128711800-128719800	Weak transcription	HSMMtube	muscle
30	chr6:128711800-128722000	Weak transcription	Osteobl	bone
31	chr6:128712000-128731800	Weak transcription	HUVEC	blood vessel
32	chr6:128712000-128733800	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:128712400-128716400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:128712400-128717800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links