Variant report

Variant	rs685330
Chromosome Location	chr1:212740145-212740146
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212729491..212744666-chr1:212778733..212791648,68	K562	blood:
2	chr1:212729172..212744062-chr1:212776412..212791648,77	K562	blood:
3	chr1:212739547..212742798-chr1:212745157..212747999,4	K562	blood:

Variant related genes	Relation type
ENSG00000264590	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1195474	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1617473	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2137424	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3106401	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3125291	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs493894	0.92[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs556847	0.84[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap]
rs585428	0.80[CHD][hapmap]
rs599028	0.80[CHD][hapmap];0.83[JPT][hapmap]
rs631569	0.81[CHD][hapmap];0.83[JPT][hapmap]

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	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212733000-212740600	Weak transcription	Fetal Heart	heart
2	chr1:212739600-212740200	Enhancers	Lung	lung
3	chr1:212739600-212740400	Flanking Active TSS	GM12878-XiMat	blood
4	chr1:212739600-212740400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr1:212739600-212741000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:212739600-212741000	Flanking Active TSS	Hela-S3	cervix
7	chr1:212739800-212740200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
8	chr1:212739800-212740200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:212739800-212740200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:212739800-212740200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:212739800-212740200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:212739800-212740200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr1:212739800-212740200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
14	chr1:212739800-212740200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:212739800-212740200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:212739800-212740200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:212739800-212740200	Flanking Active TSS	Brain Angular Gyrus	brain
18	chr1:212739800-212740200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
19	chr1:212739800-212740200	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr1:212739800-212740200	Flanking Active TSS	Pancreas	Pancrea
21	chr1:212739800-212740200	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr1:212739800-212740200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr1:212739800-212740200	Enhancers	Stomach Mucosa	stomach
24	chr1:212739800-212740400	Active TSS	Liver	Liver
25	chr1:212739800-212740400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr1:212739800-212740400	Flanking Active TSS	HepG2	liver
27	chr1:212739800-212740600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:212739800-212740600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr1:212739800-212740600	Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr1:212739800-212740600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:212739800-212740600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:212739800-212740600	Active TSS	Brain Hippocampus Middle	brain
33	chr1:212739800-212740600	Active TSS	Colonic Mucosa	Colon
34	chr1:212739800-212740600	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr1:212739800-212740600	Active TSS	Right Ventricle	heart
36	chr1:212739800-212740600	Flanking Active TSS	HSMM	muscle
37	chr1:212739800-212740600	Flanking Active TSS	NHLF	lung
38	chr1:212739800-212740800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:212739800-212740800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:212739800-212740800	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr1:212739800-212740800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr1:212739800-212740800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr1:212739800-212740800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr1:212739800-212740800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr1:212739800-212740800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:212739800-212740800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:212739800-212740800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr1:212739800-212740800	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr1:212739800-212740800	Active TSS	Brain Cingulate Gyrus	brain
50	chr1:212739800-212740800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links