Variant report

Variant	rs7555528
Chromosome Location	chr1:209953633-209953634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:209953484-209954181	GM12892	blood:	n/a	n/a
2	MTA3	chr1:209953509-209954215	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:209953604-209953821	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr1:209953569-209954049	GM12891	blood:	n/a	n/a
5	POLR2A	chr1:209952928-209958954	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:209953564-209954085	HL-60	blood:	n/a	n/a
7	POLR2A	chr1:209953478-209958346	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:209953422-209954133	GM12892	blood:	n/a	n/a
9	POLR2A	chr1:209953517-209954152	GM12892	blood:	n/a	n/a
10	POLR2A	chr1:209952746-209958845	GM12891	blood:	n/a	n/a
11	POLR2A	chr1:209953473-209954184	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209947985..209951764-chr1:209952095..209954768,3	K562	blood:
2	chr1:209953015..209954990-chr1:209956352..209958315,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSD11B1-3	chr1:209951712-209953951	NONHSAT009244

No data

Variant related genes	Relation type
TRAF3IP3	TF binding region
ENSG00000009790	Chromatin interaction
ENSG00000162757	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17389541	0.93[YRI][hapmap]
rs34540624	1.00[EUR][1000 genomes]
rs58161850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59510838	1.00[EUR][1000 genomes]
rs61578995	1.00[EUR][1000 genomes]
rs6664908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093803	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093807	1.00[EUR][1000 genomes]
rs7533957	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209942800-209956800	Weak transcription	Small Intestine	intestine
2	chr1:209942800-209957200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:209943600-209956600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:209943800-209954600	Weak transcription	NHEK	skin
5	chr1:209943800-209956600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:209943800-209956600	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:209943800-209957000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:209943800-209957200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:209944000-209956000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:209944000-209956600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:209944600-209954400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:209944800-209955200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:209944800-209956600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:209944800-209956600	Weak transcription	Right Ventricle	heart
15	chr1:209945000-209953800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:209945000-209956000	Weak transcription	Brain Anterior Caudate	brain
17	chr1:209945000-209956400	Weak transcription	Left Ventricle	heart
18	chr1:209945000-209956600	Weak transcription	Adipose Nuclei	Adipose
19	chr1:209945000-209956600	Weak transcription	Brain Angular Gyrus	brain
20	chr1:209945000-209956600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:209945000-209956600	Weak transcription	Esophagus	oesophagus
22	chr1:209945000-209956600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:209945000-209956800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:209945000-209956800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:209945200-209954600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:209945200-209956600	Weak transcription	Colonic Mucosa	Colon
27	chr1:209945200-209956600	Weak transcription	Pancreas	Pancrea
28	chr1:209945200-209957200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:209945400-209954600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:209945400-209956400	Weak transcription	Lung	lung
31	chr1:209945600-209955800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:209945600-209956400	Weak transcription	Gastric	stomach
33	chr1:209945600-209956600	Weak transcription	Fetal Lung	lung
34	chr1:209945800-209956600	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:209946000-209955800	Weak transcription	K562	blood
36	chr1:209946000-209956000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:209946000-209956600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:209946000-209956600	Strong transcription	Fetal Thymus	thymus
39	chr1:209946200-209954600	Weak transcription	Fetal Stomach	stomach
40	chr1:209946200-209956600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:209946400-209956000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:209946400-209956800	Strong transcription	Primary hematopoietic stem cells	blood
43	chr1:209946600-209956400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:209947200-209956400	Strong transcription	Dnd41	blood
45	chr1:209947600-209956600	Strong transcription	Thymus	Thymus
46	chr1:209948800-209956200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr1:209948800-209956400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:209949000-209953800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:209949000-209954600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:209949200-209956200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links