Variant report

Variant	rs6429596
Chromosome Location	chr1:46772619-46772620
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:46772400-46772717	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:46772398-46772645	GM12878	blood:	n/a	n/a
3	YY1	chr1:46772492-46772760	K562	blood:	n/a	n/a
4	WRNIP1	chr1:46772502-46772677	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:46772455-46772970	K562	blood:	n/a	n/a
6	POLR2A	chr1:46772495-46772822	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:46772412-46772885	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:46772395-46772957	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:46772346-46773287	GM12892	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46763061..46775715-chr1:46803221..46815018,50	K562	blood:
2	chr1:46771936..46775250-chr1:46797276..46800956,3	K562	blood:
3	chr1:46763061..46775205-chr1:46803159..46817121,53	K562	blood:
4	chr1:46772105..46774260-chr1:46775908..46778460,3	MCF-7	breast:
5	chr1:46767029..46769765-chr1:46770513..46776253,5	MCF-7	breast:

No data

Variant related genes	Relation type
LRRC41	TF binding region
UQCRH	TF binding region
ENSG00000132128	Chromatin interaction
ENSG00000173660	Chromatin interaction
ENSG00000117481	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10789488	0.91[AMR][1000 genomes]
rs10890386	0.88[AMR][1000 genomes]
rs10890387	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10890388	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10890389	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11584233	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11586229	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12039667	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12044708	0.86[AMR][1000 genomes]
rs12125573	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1547180	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2093044	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4660343	0.81[AMR][1000 genomes]
rs4660918	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4660919	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4660920	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4660921	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7527133	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][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	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv470711	chr1:46660295-46810530	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv947254	chr1:46769363-46808918	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46766600-46773000	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:46770400-46773000	Enhancers	Liver	Liver
3	chr1:46770400-46775400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:46770600-46773000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:46770600-46773000	Weak transcription	Brain Anterior Caudate	brain
6	chr1:46770600-46773000	Enhancers	Fetal Thymus	thymus
7	chr1:46770600-46773200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:46770600-46773200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr1:46770600-46773200	Enhancers	Fetal Heart	heart
10	chr1:46770600-46773600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr1:46770600-46773800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:46770600-46774000	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr1:46770600-46774600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:46770600-46774800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:46770600-46775400	Weak transcription	Fetal Kidney	kidney
16	chr1:46770600-46775400	Weak transcription	Spleen	Spleen
17	chr1:46770600-46775600	Weak transcription	HSMMtube	muscle
18	chr1:46770600-46781000	Strong transcription	Fetal Intestine Small	intestine
19	chr1:46770600-46783600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:46770800-46772800	Weak transcription	Fetal Brain Female	brain
21	chr1:46770800-46773200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:46770800-46773200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:46770800-46773200	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr1:46770800-46773200	Weak transcription	Osteobl	bone
25	chr1:46770800-46773400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:46770800-46774800	Weak transcription	NHLF	lung
27	chr1:46770800-46775400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:46770800-46775400	Weak transcription	Small Intestine	intestine
29	chr1:46770800-46775600	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:46770800-46775600	Weak transcription	NHDF-Ad	bronchial
31	chr1:46770800-46787000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:46771000-46773000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:46771000-46773000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr1:46771000-46773000	Strong transcription	Fetal Stomach	stomach
35	chr1:46771000-46773200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:46771000-46773200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr1:46771000-46773400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:46771000-46773400	Enhancers	Stomach Smooth Muscle	stomach
39	chr1:46771000-46774000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:46771000-46774200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr1:46771000-46774600	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr1:46771000-46774600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:46771000-46774600	Weak transcription	HMEC	breast
44	chr1:46771000-46774800	Weak transcription	Fetal Lung	lung
45	chr1:46771000-46774800	Weak transcription	HSMM	muscle
46	chr1:46771000-46775000	Weak transcription	Esophagus	oesophagus
47	chr1:46771000-46775400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:46771000-46775400	Weak transcription	Aorta	Aorta
49	chr1:46771000-46775600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:46771000-46775600	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links