Variant report

Variant	rs6671220
Chromosome Location	chr1:246912124-246912125
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246911249..246913997-chr1:246914503..246916490,2	K562	blood:
2	chr1:246867885..246870245-chr1:246910384..246912809,2	MCF-7	breast:
3	chr1:246886275..246889143-chr1:246911120..246913975,3	MCF-7	breast:
4	chr1:246887255..246889228-chr1:246910662..246914076,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143653	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10924816	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10924827	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11581735	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12023715	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12026095	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12042435	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703972	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3314	0.86[EUR][1000 genomes]
rs41267531	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56338592	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56975801	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57384976	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58542205	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60107954	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6426330	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7414184	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7417422	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv870294	chr1:246877043-246927940	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
2	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:246889000-246929000	Weak transcription	Stomach Mucosa	stomach
4	chr1:246890200-246913200	Strong transcription	Fetal Muscle Leg	muscle
5	chr1:246890600-246914000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:246892600-246924400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:246893800-246912800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:246894600-246923800	Weak transcription	Pancreas	Pancrea
9	chr1:246895000-246942200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:246895400-246938600	Weak transcription	Fetal Heart	heart
11	chr1:246896400-246917000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:246897600-246912400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:246900000-246917600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:246900800-246912200	Weak transcription	Esophagus	oesophagus
15	chr1:246901200-246924000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:246902600-246912200	Weak transcription	Lung	lung
17	chr1:246902800-246923200	Weak transcription	Fetal Brain Male	brain
18	chr1:246902800-246923800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:246903000-246917200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:246904600-246942800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr1:246905000-246922200	Weak transcription	Brain Germinal Matrix	brain
23	chr1:246905000-246922200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr1:246905000-246923600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:246905000-246923800	Weak transcription	Thymus	Thymus
26	chr1:246905000-246924000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:246905000-246945800	Weak transcription	Psoas Muscle	Psoas
28	chr1:246905600-246923400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:246905600-246923800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:246905800-246923800	Weak transcription	Colonic Mucosa	Colon
31	chr1:246905800-246931600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:246906000-246923800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:246906200-246917200	Weak transcription	GM12878-XiMat	blood
34	chr1:246906600-246914000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:246906800-246923000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr1:246906800-246923800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:246907000-246923600	Weak transcription	Aorta	Aorta
38	chr1:246907400-246922200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:246908000-246913600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr1:246908600-246923400	Weak transcription	NH-A	brain
41	chr1:246908600-246923800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:246908800-246922200	Weak transcription	Brain Substantia Nigra	brain
43	chr1:246908800-246922600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:246908800-246922600	Weak transcription	NHLF	lung
45	chr1:246908800-246923000	Weak transcription	HUVEC	blood vessel
46	chr1:246908800-246923600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:246908800-246923600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:246908800-246923800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:246909000-246912200	Weak transcription	K562	blood
50	chr1:246909000-246912200	Weak transcription	Osteobl	bone

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