Variant report

Variant	rs6669006
Chromosome Location	chr1:113562386-113562387
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113540112..113542991-chr1:113560118..113562958,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1216774	0.86[ASN][1000 genomes]
rs1216776	0.86[ASN][1000 genomes]
rs1216778	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17494145	0.95[EUR][1000 genomes]
rs17494180	0.97[EUR][1000 genomes]
rs4839276	0.88[EUR][1000 genomes]
rs4839277	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55768060	0.92[EUR][1000 genomes]
rs55982206	0.87[EUR][1000 genomes]
rs56019044	0.88[EUR][1000 genomes]
rs72683454	0.80[EUR][1000 genomes]
rs72683459	0.87[EUR][1000 genomes]
rs72683463	0.98[EUR][1000 genomes]
rs72683468	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer 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	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
10	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6669006	SLC16A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113511200-113564000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr1:113526600-113564200	Weak transcription	Placenta	Placenta
3	chr1:113535800-113564000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:113535800-113564000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:113535800-113564200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:113535800-113568800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:113539600-113564200	Weak transcription	Brain Germinal Matrix	brain
8	chr1:113541000-113573800	Weak transcription	Right Ventricle	heart
9	chr1:113541600-113564200	Weak transcription	Osteobl	bone
10	chr1:113541800-113564000	Weak transcription	K562	blood
11	chr1:113542000-113564000	Weak transcription	Hela-S3	cervix
12	chr1:113543200-113574400	Weak transcription	HSMM	muscle
13	chr1:113547400-113564000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:113550800-113563400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:113551000-113564000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:113551200-113563200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:113551200-113564000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:113551200-113564000	Weak transcription	HMEC	breast
19	chr1:113551200-113564200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:113551200-113564400	Weak transcription	Adipose Nuclei	Adipose
21	chr1:113551200-113569800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:113551200-113569800	Weak transcription	Left Ventricle	heart
23	chr1:113552800-113564000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:113552800-113570200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:113553000-113572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:113554400-113564000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:113555200-113563400	Weak transcription	NHEK	skin
28	chr1:113555600-113572200	Weak transcription	Primary T cells from cord blood	blood
29	chr1:113555600-113584200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:113556800-113564200	Weak transcription	Fetal Intestine Large	intestine
31	chr1:113556800-113564200	Weak transcription	Fetal Intestine Small	intestine
32	chr1:113561400-113564000	Enhancers	HepG2	liver
33	chr1:113561600-113562400	Enhancers	Duodenum Mucosa	Duodenum
34	chr1:113561800-113563000	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr1:113562200-113562600	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr1:113562200-113563400	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links