Variant report

Variant	rs13143989
Chromosome Location	chr4:129759695-129759696
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:129739255..129743318-chr4:129756229..129760124,4	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10518538	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10857133	1.00[CHB][hapmap]
rs11098988	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098989	0.94[ASN][1000 genomes]
rs11098991	0.83[ASN][1000 genomes]
rs11722253	1.00[CHB][hapmap]
rs11722830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11730068	0.85[ASN][1000 genomes]
rs11734137	0.86[ASN][1000 genomes]
rs11735343	1.00[CHB][hapmap]
rs11736731	1.00[CHB][hapmap]
rs11933240	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs11940298	0.94[ASN][1000 genomes]
rs11945441	0.88[ASN][1000 genomes]
rs12505447	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13110855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs13110952	0.85[ASN][1000 genomes]
rs13110956	0.81[ASN][1000 genomes]
rs13111413	1.00[CHB][hapmap]
rs13114904	0.94[ASN][1000 genomes]
rs13125643	0.94[ASN][1000 genomes]
rs13135764	0.83[ASN][1000 genomes]
rs13136807	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13139971	0.94[ASN][1000 genomes]
rs13146706	0.83[ASN][1000 genomes]
rs13149221	1.00[CHB][hapmap]
rs13150960	0.80[EUR][1000 genomes]
rs13151322	0.81[CHB][hapmap]
rs17013734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129746600-129761800	Strong transcription	Dnd41	blood
2	chr4:129746800-129770200	Weak transcription	HMEC	breast
3	chr4:129747000-129766600	Weak transcription	NHEK	skin
4	chr4:129747400-129761600	Weak transcription	Placenta	Placenta
5	chr4:129748000-129761600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:129752400-129763800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:129752600-129761800	Strong transcription	Fetal Thymus	thymus
8	chr4:129752800-129760600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:129753000-129761000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr4:129753000-129766200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:129753200-129763800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:129753200-129767600	Weak transcription	Colonic Mucosa	Colon
13	chr4:129753400-129764000	Weak transcription	Fetal Brain Female	brain
14	chr4:129753400-129766000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:129753400-129767600	Weak transcription	Fetal Brain Male	brain
16	chr4:129753600-129767600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr4:129753600-129798600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:129753800-129759800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr4:129753800-129770400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:129753800-129795000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:129754000-129761600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr4:129754400-129770600	Weak transcription	Fetal Kidney	kidney
23	chr4:129755000-129763000	Enhancers	Fetal Heart	heart
24	chr4:129755400-129761000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
25	chr4:129755400-129764800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr4:129756600-129763800	Weak transcription	Hela-S3	cervix
27	chr4:129756800-129761600	Weak transcription	HUVEC	blood vessel
28	chr4:129756800-129763800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:129756800-129764200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr4:129757000-129764600	Weak transcription	Brain Angular Gyrus	brain
31	chr4:129757000-129770000	Weak transcription	Small Intestine	intestine
32	chr4:129757200-129760000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:129757200-129761400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:129757200-129761600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:129757200-129761600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:129757200-129761600	Weak transcription	Lung	lung
37	chr4:129757200-129762400	Weak transcription	Esophagus	oesophagus
38	chr4:129757200-129762600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr4:129757200-129763200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr4:129757200-129763800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr4:129757200-129763800	Weak transcription	Brain Anterior Caudate	brain
42	chr4:129757200-129764000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr4:129757200-129764000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr4:129757200-129764200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:129757200-129764200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:129757200-129764200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr4:129757200-129764400	Weak transcription	HSMMtube	muscle
48	chr4:129757200-129764600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr4:129757200-129765000	Weak transcription	Spleen	Spleen
50	chr4:129757200-129765200	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links