Variant report

Variant	rs6042178
Chromosome Location	chr20:13481031-13481032
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs2038436	1.00[AMR][1000 genomes]
rs28445300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35357303	1.00[AMR][1000 genomes]
rs3945993	1.00[AMR][1000 genomes]
rs6033700	1.00[AMR][1000 genomes]
rs6033711	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6033713	1.00[AMR][1000 genomes]
rs6042062	1.00[AMR][1000 genomes]
rs6042100	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042112	1.00[AMR][1000 genomes]
rs6042114	1.00[AMR][1000 genomes]
rs6042115	1.00[AMR][1000 genomes]
rs6042122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042125	1.00[AMR][1000 genomes]
rs6042129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042144	1.00[AMR][1000 genomes]
rs6042161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042166	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042173	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042191	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6042193	1.00[AMR][1000 genomes]
rs6042200	1.00[AMR][1000 genomes]
rs6042215	1.00[AMR][1000 genomes]
rs6042216	1.00[AMR][1000 genomes]
rs6042217	1.00[AMR][1000 genomes]
rs6105112	1.00[AMR][1000 genomes]
rs6105114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6105122	1.00[AMR][1000 genomes]
rs6109851	1.00[AMR][1000 genomes]
rs6109852	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6109853	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6109855	1.00[AMR][1000 genomes]
rs6109856	1.00[AMR][1000 genomes]
rs6109857	1.00[AMR][1000 genomes]
rs6109860	1.00[AMR][1000 genomes]
rs6109874	1.00[AMR][1000 genomes]
rs6109878	1.00[AMR][1000 genomes]
rs6109880	1.00[AMR][1000 genomes]
rs6109881	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6109897	1.00[AMR][1000 genomes]
rs6109919	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6109943	1.00[AMR][1000 genomes]
rs6109944	1.00[AMR][1000 genomes]
rs6109948	1.00[AMR][1000 genomes]
rs6109956	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv585435	chr20:13410638-13582476	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv458871	chr20:13447896-13573415	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv585436	chr20:13447896-13573415	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	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

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13463800-13481200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr20:13463800-13505400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr20:13464000-13493800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr20:13464200-13483400	Weak transcription	Fetal Thymus	thymus
5	chr20:13468000-13483600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr20:13468200-13481200	Weak transcription	Liver	Liver
7	chr20:13468200-13483600	Weak transcription	Right Ventricle	heart
8	chr20:13470200-13505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr20:13471800-13483400	Weak transcription	Fetal Intestine Small	intestine
10	chr20:13473400-13505800	Weak transcription	HSMM	muscle
11	chr20:13474000-13482000	Weak transcription	HMEC	breast
12	chr20:13474200-13482600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr20:13474400-13483000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr20:13474400-13483600	Weak transcription	Left Ventricle	heart
15	chr20:13474400-13496800	Weak transcription	Pancreas	Pancrea
16	chr20:13477400-13484000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr20:13478200-13503800	Weak transcription	Gastric	stomach
18	chr20:13479000-13482000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr20:13479000-13483400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr20:13479200-13481400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr20:13479200-13486200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr20:13479400-13481800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
23	chr20:13479400-13483400	Weak transcription	Aorta	Aorta
24	chr20:13479600-13481400	ZNF genes & repeats	Fetal Intestine Large	intestine
25	chr20:13479600-13483400	Weak transcription	Fetal Stomach	stomach
26	chr20:13479800-13481200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr20:13480000-13481600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr20:13480000-13482200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
29	chr20:13480000-13482400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr20:13480000-13488200	Weak transcription	NHEK	skin
31	chr20:13480000-13490400	ZNF genes & repeats	Dnd41	blood
32	chr20:13480200-13483400	Weak transcription	Ovary	ovary
33	chr20:13480200-13484400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr20:13480400-13483400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr20:13480400-13483400	Weak transcription	Thymus	Thymus
36	chr20:13480600-13481200	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr20:13480600-13481400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
38	chr20:13480800-13483200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr20:13480800-13483400	Weak transcription	Primary B cells from cord blood	blood

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