Variant report

Variant	rs2406709
Chromosome Location	chr13:48626116-48626117
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:48621450..48623489-chr13:48625313..48627091,2	K562	blood:
2	chr13:48610411..48612225-chr13:48624837..48627697,2	K562	blood:
3	chr13:48619636..48622232-chr13:48625970..48628449,2	K562	blood:

Variant related genes	Relation type
ENSG00000136159	Chromatin interaction
ENSG00000136143	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11616639	0.85[ASN][1000 genomes]
rs1410117	0.92[ASN][1000 genomes]
rs1571256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1927213	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2094192	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2104480	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2148246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2406797	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4294712	0.91[ASN][1000 genomes]
rs4369555	0.95[JPT][hapmap]
rs4941623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4942748	0.95[ASN][1000 genomes]
rs56399021	0.94[ASN][1000 genomes]
rs7324484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7326363	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7333247	0.83[ASN][1000 genomes]
rs7336214	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8001243	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9526407	0.82[JPT][hapmap]
rs9526442	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9526443	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9526445	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9526447	0.92[ASN][1000 genomes]
rs9526449	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526451	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9534888	0.95[JPT][hapmap]
rs9534931	0.86[ASN][1000 genomes]
rs9534932	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9534933	0.93[ASN][1000 genomes]
rs9534937	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9534939	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9534943	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534945	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534946	0.93[ASN][1000 genomes]
rs9534947	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9534948	0.93[ASN][1000 genomes]
rs9534949	0.88[ASN][1000 genomes]
rs9534950	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9534951	0.89[ASN][1000 genomes]
rs9534952	0.91[ASN][1000 genomes]
rs9534957	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9534961	0.83[ASN][1000 genomes]
rs9534965	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9562802	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9567987	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9567991	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9567994	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs9568000	0.85[ASN][1000 genomes]
rs9568014	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers 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 miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48612600-48631600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:48612600-48640400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr13:48612600-48645000	Weak transcription	Stomach Mucosa	stomach
4	chr13:48612800-48628000	Weak transcription	Fetal Brain Male	brain
5	chr13:48612800-48640200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr13:48612800-48640400	Weak transcription	Psoas Muscle	Psoas
7	chr13:48613000-48640200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr13:48613000-48640400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr13:48613200-48626600	Weak transcription	Right Ventricle	heart
10	chr13:48613200-48629000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:48613200-48631800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr13:48613200-48640400	Weak transcription	Fetal Heart	heart
13	chr13:48613200-48641600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr13:48613200-48642200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr13:48613400-48641600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr13:48613400-48647000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr13:48613600-48636400	Weak transcription	Hela-S3	cervix
18	chr13:48613600-48645000	Weak transcription	Small Intestine	intestine
19	chr13:48614400-48627600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr13:48614400-48628600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr13:48614400-48636400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr13:48614800-48628200	Strong transcription	Dnd41	blood
23	chr13:48616400-48626600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr13:48616400-48626600	Weak transcription	Pancreas	Pancrea
25	chr13:48616400-48642800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr13:48616600-48626600	Weak transcription	Fetal Lung	lung
27	chr13:48617600-48626600	Weak transcription	Esophagus	oesophagus
28	chr13:48618800-48626200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr13:48618800-48644800	Weak transcription	Colonic Mucosa	Colon
30	chr13:48619200-48628200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr13:48619600-48627400	Strong transcription	Fetal Thymus	thymus
32	chr13:48619600-48630200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr13:48619800-48628400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr13:48620000-48628400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr13:48620000-48629000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr13:48620000-48629000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr13:48620200-48628600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr13:48620200-48629600	Strong transcription	Fetal Intestine Large	intestine
39	chr13:48620200-48630400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr13:48620400-48627800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr13:48620800-48627800	Strong transcription	Fetal Muscle Leg	muscle
42	chr13:48621000-48629000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr13:48621400-48627600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr13:48621400-48628800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr13:48621400-48629000	Strong transcription	Liver	Liver
46	chr13:48621600-48627600	Strong transcription	Primary T cells from cord blood	blood
47	chr13:48621600-48627600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr13:48621600-48628800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr13:48621800-48627800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr13:48621800-48628200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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