Variant report

Variant	rs1999112
Chromosome Location	chr20:13770673-13770674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:13770648-13771277	HepG2	liver:	n/a	n/a
2	POLR2A	chr20:13770530-13770906	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:13769397..13772181-chr20:13776678..13779154,2	K562	blood:
2	chr20:13769039..13770895-chr20:13773639..13775418,2	K562	blood:
3	chr20:13770594..13773511-chr20:13777159..13778904,2	MCF-7	breast:
4	chr20:13769074..13771240-chr20:13798879..13801315,2	K562	blood:

Variant related genes	Relation type
NDUFAF5	TF binding region
ENSG00000101247	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs13039364	0.89[CEU][hapmap];0.88[CHB][hapmap]
rs13042637	0.88[ASN][1000 genomes]
rs1547920	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2031933	0.90[ASN][1000 genomes]
rs2209993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2209994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2327797	0.94[CEU][hapmap];0.88[CHB][hapmap]
rs2423745	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2423749	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2423750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2423753	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3180370	0.88[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.90[ASN][1000 genomes]
rs34449907	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34806363	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35361761	0.81[ASN][1000 genomes]
rs35632254	0.81[ASN][1000 genomes]
rs4813139	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs4813142	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4814258	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6033809	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs6033816	0.90[ASN][1000 genomes]
rs6033819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6033821	0.88[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.91[ASN][1000 genomes]
rs6042324	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs6042336	0.88[CHB][hapmap]
rs6042351	0.83[ASN][1000 genomes]
rs6042357	0.89[ASN][1000 genomes]
rs6042362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6074637	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs6074643	0.94[CEU][hapmap];0.88[CHB][hapmap];0.90[ASN][1000 genomes]
rs6074644	0.94[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6079154	0.88[CHB][hapmap]
rs6079156	0.94[CEU][hapmap];0.86[CHB][hapmap]
rs6079158	0.94[CEU][hapmap];0.88[CHB][hapmap]
rs6079162	0.88[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap]
rs6079165	0.84[ASN][1000 genomes]
rs6079166	0.94[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6079176	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079178	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079181	0.94[CEU][hapmap];0.88[CHB][hapmap];0.85[GIH][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6079182	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6105162	0.85[ASN][1000 genomes]
rs6110026	0.88[CHB][hapmap]
rs6110035	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6134968	0.83[ASN][1000 genomes]
rs62209178	0.84[ASN][1000 genomes]
rs62209207	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68012295	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7265467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs754796	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13766400-13793800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:13766400-13796800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:13766600-13772200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr20:13766800-13781400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr20:13767200-13770800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr20:13767200-13771000	Weak transcription	Primary B cells from cord blood	blood
7	chr20:13767200-13771400	Weak transcription	Fetal Kidney	kidney
8	chr20:13767400-13770800	Weak transcription	Ovary	ovary
9	chr20:13767400-13771000	Weak transcription	Aorta	Aorta
10	chr20:13767400-13771400	Weak transcription	Right Ventricle	heart
11	chr20:13767400-13771800	Weak transcription	Pancreas	Pancrea
12	chr20:13767400-13772400	Weak transcription	Esophagus	oesophagus
13	chr20:13767400-13792600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr20:13767600-13770800	Weak transcription	Brain Anterior Caudate	brain
15	chr20:13767600-13771200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr20:13767600-13772400	Weak transcription	Right Atrium	heart
17	chr20:13767600-13775200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr20:13767600-13775200	Weak transcription	Small Intestine	intestine
19	chr20:13767600-13789800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr20:13767600-13799600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr20:13767800-13770800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr20:13767800-13770800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr20:13767800-13771400	Strong transcription	Left Ventricle	heart
24	chr20:13767800-13799400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr20:13767800-13800600	Weak transcription	Stomach Mucosa	stomach
26	chr20:13768000-13771800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr20:13768000-13773400	Strong transcription	HUVEC	blood vessel
28	chr20:13768000-13778400	Strong transcription	Fetal Muscle Leg	muscle
29	chr20:13768000-13780600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr20:13768000-13781400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr20:13768000-13786000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr20:13768000-13794800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr20:13768000-13799800	Strong transcription	Fetal Thymus	thymus
34	chr20:13768200-13771200	Weak transcription	Fetal Brain Male	brain
35	chr20:13768200-13771600	Weak transcription	Hela-S3	cervix
36	chr20:13768200-13776600	Strong transcription	NH-A	brain
37	chr20:13768200-13780000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr20:13768200-13780000	Strong transcription	Placenta	Placenta
39	chr20:13768200-13780400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr20:13768200-13799800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr20:13768200-13799800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr20:13768400-13774000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr20:13768400-13799600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr20:13768600-13778000	Strong transcription	Fetal Lung	lung
45	chr20:13768600-13799600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr20:13768800-13771000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr20:13768800-13771400	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr20:13768800-13774600	Strong transcription	K562	blood
49	chr20:13768800-13780400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr20:13768800-13786200	Strong transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links