Variant report

Variant	rs71648448
Chromosome Location	chr1:228104257-228104258
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228104214..228105732-chr1:228108237..228110826,2	MCF-7	breast:
2	chr1:228102507..228105005-chr1:228106646..228109537,2	MCF-7	breast:
3	chr1:228102020..228104817-chr1:228104964..228106972,3	K562	blood:

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11585054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12725747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12726048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34253719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34418349	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35718701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35834046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71648447	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs71650367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
7	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
8	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
10	nsv873250	chr1:228051234-228121548	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv873251	chr1:228051234-228160911	Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
12	esv3453192	chr1:228102029-228106627	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv3453193	chr1:228102029-228106627	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv3426585	chr1:228102929-228105827	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv3415950	chr1:228103129-228105627	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228075600-228109200	Weak transcription	Right Atrium	heart
2	chr1:228096400-228104400	Weak transcription	Gastric	stomach
3	chr1:228098600-228108600	Weak transcription	Fetal Intestine Small	intestine
4	chr1:228098600-228117600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:228098800-228122800	Weak transcription	HSMMtube	muscle
6	chr1:228099200-228108400	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:228099400-228108800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:228099400-228122400	Weak transcription	HSMM	muscle
9	chr1:228100200-228105600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:228100400-228105800	Enhancers	Fetal Stomach	stomach
11	chr1:228100600-228105000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:228100600-228105400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr1:228100600-228105800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr1:228100600-228108200	Enhancers	Fetal Muscle Leg	muscle
15	chr1:228100800-228104800	Enhancers	Esophagus	oesophagus
16	chr1:228100800-228105600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr1:228101200-228104400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:228101200-228110400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:228101400-228104400	Weak transcription	Fetal Kidney	kidney
20	chr1:228101400-228105800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:228101400-228111000	Weak transcription	Fetal Brain Female	brain
22	chr1:228101600-228105800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:228102000-228105400	Weak transcription	Right Ventricle	heart
24	chr1:228102200-228105200	Enhancers	HMEC	breast
25	chr1:228102400-228104400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:228102400-228106800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:228102400-228108600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:228102600-228108400	Enhancers	Fetal Muscle Trunk	muscle
29	chr1:228102800-228104400	Enhancers	NHEK	skin
30	chr1:228103000-228104400	Weak transcription	Spleen	Spleen
31	chr1:228103000-228104800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:228103000-228105200	Weak transcription	Ovary	ovary
33	chr1:228103000-228107400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:228103400-228104800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:228103400-228107400	Weak transcription	Pancreas	Pancrea
36	chr1:228103600-228105200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:228103600-228106800	Enhancers	Brain Hippocampus Middle	brain
38	chr1:228103800-228104400	Enhancers	Brain Anterior Caudate	brain
39	chr1:228103800-228104400	Enhancers	Brain Substantia Nigra	brain
40	chr1:228103800-228104800	Genic enhancers	Stomach Smooth Muscle	stomach
41	chr1:228103800-228107400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:228103800-228113800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr1:228103800-228117000	Weak transcription	Fetal Intestine Large	intestine
44	chr1:228104000-228104400	ZNF genes & repeats	Lung	lung
45	chr1:228104000-228104400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
46	chr1:228104000-228104600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:228104000-228104600	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:228104000-228104800	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr1:228104000-228105400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:228104000-228105400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links