Variant report

Variant	rs6689022
Chromosome Location	chr1:154904230-154904231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154850056..154852682-chr1:154903933..154905463,2	MCF-7	breast:
2	chr1:154902125..154904691-chr1:154910364..154912646,2	K562	blood:
3	chr1:154900011..154901853-chr1:154902099..154904633,2	K562	blood:
4	chr1:154901654..154906164-chr1:154907018..154910146,5	K562	blood:
5	chr1:154903050..154905621-chr1:154907770..154910146,3	K562	blood:
6	chr1:154903245..154906216-chr1:154928700..154931455,2	K562	blood:
7	chr1:154886112..154888306-chr1:154903481..154905396,2	K562	blood:
8	chr1:154897179..154899202-chr1:154902262..154904996,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163344	Chromatin interaction
ENSG00000270361	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10908448	0.96[YRI][hapmap]
rs11264286	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11264287	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11581175	1.00[CEU][hapmap]
rs11799384	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1218582	0.88[YRI][hapmap]
rs1580943	0.92[YRI][hapmap]
rs16836521	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1891805	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2102423	0.92[YRI][hapmap]
rs2174507	0.92[YRI][hapmap]
rs2211498	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2335408	0.96[YRI][hapmap]
rs34215800	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4240874	0.80[AFR][1000 genomes]
rs4845398	0.85[YRI][hapmap]
rs4845690	0.96[YRI][hapmap]
rs55887894	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56720968	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6696628	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6699043	0.96[YRI][hapmap]
rs7539805	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7543051	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7551495	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs869506	0.96[YRI][hapmap]
rs877343	0.92[YRI][hapmap]
rs906593	0.92[YRI][hapmap]

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	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv464073	chr1:154837796-154904840	Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv547960	chr1:154837796-154904840	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv2977	chr1:154881053-154907613	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154884800-154908400	Weak transcription	Psoas Muscle	Psoas
2	chr1:154886800-154908200	Weak transcription	Fetal Heart	heart
3	chr1:154891200-154908600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:154892600-154905400	Strong transcription	Fetal Muscle Leg	muscle
5	chr1:154893200-154905600	Strong transcription	Stomach Smooth Muscle	stomach
6	chr1:154893200-154908200	Weak transcription	NH-A	brain
7	chr1:154893400-154905600	Strong transcription	Fetal Stomach	stomach
8	chr1:154894200-154905000	Strong transcription	Fetal Brain Female	brain
9	chr1:154894400-154904800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:154894400-154908400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:154894600-154905000	Strong transcription	Fetal Muscle Trunk	muscle
12	chr1:154894800-154904800	Strong transcription	Esophagus	oesophagus
13	chr1:154894800-154904800	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:154894800-154905000	Strong transcription	Adipose Nuclei	Adipose
15	chr1:154894800-154905000	Strong transcription	Brain Germinal Matrix	brain
16	chr1:154894800-154905000	Strong transcription	GM12878-XiMat	blood
17	chr1:154895000-154905000	Strong transcription	Brain Hippocampus Middle	brain
18	chr1:154895000-154907600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:154895800-154904600	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:154895800-154904600	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:154895800-154908000	Weak transcription	Fetal Brain Male	brain
22	chr1:154896000-154908200	Weak transcription	HUVEC	blood vessel
23	chr1:154896800-154908600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:154898200-154908400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:154898800-154905000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:154898800-154908200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:154898800-154908200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:154898800-154908200	Weak transcription	HSMMtube	muscle
29	chr1:154899000-154905000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr1:154899000-154905200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr1:154899000-154907600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:154899000-154908200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:154899000-154908200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr1:154899200-154904800	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:154899200-154907600	Weak transcription	Dnd41	blood
36	chr1:154899200-154908200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:154899200-154908200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:154899200-154908200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:154899200-154908600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:154899200-154908800	Weak transcription	Small Intestine	intestine
41	chr1:154899400-154908200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:154899400-154908200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:154899400-154908400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:154899400-154908400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:154899600-154908200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:154899600-154908200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr1:154899600-154908200	Weak transcription	NHLF	lung
48	chr1:154900000-154904800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:154900200-154905400	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr1:154900200-154908200	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links