Variant report

Variant	rs166627
Chromosome Location	chr1:86823198-86823199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86821077..86823352-chr1:86861196..86863227,2	K562	blood:

Variant related genes	Relation type
ENSG00000122417	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10493789	0.85[ASN][1000 genomes]
rs10747328	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10873777	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1158505	0.85[ASN][1000 genomes]
rs1182102	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1334143	0.85[ASN][1000 genomes]
rs1334146	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1334147	0.85[ASN][1000 genomes]
rs1334148	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs166626	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17129078	0.84[ASN][1000 genomes]
rs175363	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs187971	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1931363	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2104963	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2151708	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2151709	0.85[ASN][1000 genomes]
rs272491	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs272492	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs272494	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs272498	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs272504	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs272507	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs272510	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs272511	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs272516	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3765975	0.85[ASN][1000 genomes]
rs405424	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4288573	0.93[ASN][1000 genomes]
rs61804060	0.84[ASN][1000 genomes]
rs6695671	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs883200	0.86[ASN][1000 genomes]

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	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871866	chr1:86726619-86851420	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
5	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	esv1792405	chr1:86814270-86825639	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
7	esv3453694	chr1:86821560-86823342	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv3491391	chr1:86821606-86823327	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv3491392	chr1:86821606-86823327	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv3453695	chr1:86821628-86823273	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86806400-86823600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:86808600-86842800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:86813800-86836400	Weak transcription	Lung	lung
4	chr1:86813800-86842600	Weak transcription	Fetal Heart	heart
5	chr1:86815200-86860200	Weak transcription	Fetal Brain Male	brain
6	chr1:86816000-86842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:86816200-86824200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:86816200-86826200	Weak transcription	A549	lung
9	chr1:86817200-86843800	Weak transcription	Small Intestine	intestine
10	chr1:86817400-86824400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:86817400-86824400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:86817400-86826000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:86817400-86826000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:86817400-86826200	Strong transcription	HUVEC	blood vessel
15	chr1:86817600-86825200	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr1:86817600-86825400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:86817600-86826000	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:86817600-86826200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:86817600-86843000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:86817800-86828000	Weak transcription	Fetal Stomach	stomach
21	chr1:86817800-86828000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:86817800-86835400	Weak transcription	Esophagus	oesophagus
23	chr1:86817800-86840000	Weak transcription	GM12878-XiMat	blood
24	chr1:86817800-86842400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:86818000-86842600	Weak transcription	Fetal Intestine Small	intestine
26	chr1:86818000-86843200	Weak transcription	Pancreas	Pancrea
27	chr1:86818000-86851600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:86818200-86841000	Weak transcription	Fetal Kidney	kidney
29	chr1:86818400-86823400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:86818400-86824000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:86818800-86823600	Strong transcription	Primary T cells from cord blood	blood
32	chr1:86819000-86824000	Strong transcription	Fetal Intestine Large	intestine
33	chr1:86819000-86838400	Weak transcription	NHDF-Ad	bronchial
34	chr1:86819800-86823200	Weak transcription	Colonic Mucosa	Colon
35	chr1:86819800-86824000	Weak transcription	Right Ventricle	heart
36	chr1:86819800-86828000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:86819800-86830200	Weak transcription	Spleen	Spleen
38	chr1:86819800-86839400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:86819800-86839400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:86819800-86840200	Weak transcription	Brain Angular Gyrus	brain
41	chr1:86819800-86840200	Weak transcription	HMEC	breast
42	chr1:86819800-86842200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:86819800-86842600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:86819800-86843000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:86819800-86843000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:86820200-86823600	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:86820200-86824000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:86820200-86826800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:86820200-86840200	Weak transcription	Brain Anterior Caudate	brain
50	chr1:86820200-86841200	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links