Variant report

Variant	rs12084714
Chromosome Location	chr1:226044063-226044064
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226042077..226044688-chr1:226110090..226112065,2	MCF-7	breast:
2	chr1:226042955..226044481-chr1:226050392..226052677,2	MCF-7	breast:
3	chr1:226044051..226045596-chr1:226062360..226064718,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143811	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10915883	0.98[AFR][1000 genomes]
rs10915886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10915887	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10915888	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10915889	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10915890	0.82[AFR][1000 genomes]
rs12070110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12070816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12071072	0.82[AFR][1000 genomes]
rs12071104	0.82[AFR][1000 genomes]
rs12071413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12075664	0.97[AFR][1000 genomes]
rs12077174	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12077562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12077565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12079891	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12081742	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12082207	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12083928	1.00[AFR][1000 genomes]
rs12088057	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12097377	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2292561	0.88[AFR][1000 genomes]
rs35273824	0.81[AFR][1000 genomes]
rs35684337	0.81[AFR][1000 genomes]
rs55706532	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56112955	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56325807	0.90[AFR][1000 genomes]
rs58852301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59728172	0.90[AFR][1000 genomes]
rs60132040	0.89[AFR][1000 genomes]
rs60739570	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61304305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74150526	0.86[AFR][1000 genomes]
rs74150531	0.87[AMR][1000 genomes]
rs74150536	0.90[AFR][1000 genomes]
rs74150537	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74150538	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74150539	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv520628	chr1:226026406-226093362	Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226013600-226052600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:226014800-226047800	Weak transcription	Psoas Muscle	Psoas
3	chr1:226016000-226051000	Weak transcription	NH-A	brain
4	chr1:226017400-226049800	Weak transcription	HUVEC	blood vessel
5	chr1:226026800-226061600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:226029800-226050600	Strong transcription	Right Ventricle	heart
7	chr1:226030400-226046800	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:226030400-226052600	Weak transcription	HSMMtube	muscle
9	chr1:226033600-226053000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:226033800-226067400	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr1:226034000-226056800	Strong transcription	Adipose Nuclei	Adipose
12	chr1:226034000-226063000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:226034200-226062800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:226034600-226047600	Weak transcription	NHEK	skin
15	chr1:226036000-226049000	Weak transcription	A549	lung
16	chr1:226036600-226064600	Weak transcription	Fetal Heart	heart
17	chr1:226036800-226044800	Genic enhancers	Fetal Thymus	thymus
18	chr1:226036800-226048600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:226036800-226058600	Weak transcription	Brain Germinal Matrix	brain
20	chr1:226036800-226066600	Weak transcription	Fetal Brain Male	brain
21	chr1:226037000-226045400	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:226037000-226054200	Weak transcription	Small Intestine	intestine
23	chr1:226037400-226048600	Weak transcription	Dnd41	blood
24	chr1:226037400-226051800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:226037600-226051800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr1:226037600-226060600	Strong transcription	Placenta	Placenta
27	chr1:226037800-226045000	Strong transcription	Gastric	stomach
28	chr1:226037800-226046200	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr1:226037800-226048400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:226037800-226065200	Weak transcription	Right Atrium	heart
31	chr1:226038000-226052400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:226038400-226059600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:226038600-226054800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:226038800-226065800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:226039000-226063200	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:226039200-226045000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:226039200-226045200	Strong transcription	Aorta	Aorta
38	chr1:226039200-226064600	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:226039400-226053000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:226039400-226053200	Strong transcription	Thymus	Thymus
41	chr1:226039600-226045800	Strong transcription	Left Ventricle	heart
42	chr1:226039600-226050800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:226039600-226051200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:226039600-226053800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:226039600-226059800	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:226039600-226062200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:226039600-226063000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:226039800-226046800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr1:226039800-226050400	Strong transcription	Colon Smooth Muscle	Colon
50	chr1:226039800-226052000	Strong transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links