Variant report

Variant	rs61609910
Chromosome Location	chr7:26776096-26776097
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1023712	0.90[AFR][1000 genomes]
rs1024452	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1024453	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951146	0.90[AFR][1000 genomes]
rs10951147	0.90[AFR][1000 genomes]
rs10951148	0.84[AFR][1000 genomes]
rs1123156	0.84[AFR][1000 genomes]
rs1129771	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11773029	0.81[AFR][1000 genomes]
rs11773050	0.80[AFR][1000 genomes]
rs11971041	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971098	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11972823	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973332	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11976472	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11977233	0.90[AFR][1000 genomes]
rs11978456	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979611	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11980739	0.83[AFR][1000 genomes]
rs11982489	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700758	0.81[AFR][1000 genomes]
rs12700760	0.81[AFR][1000 genomes]
rs1468203	0.90[AFR][1000 genomes]
rs17372780	0.90[AFR][1000 genomes]
rs1859101	0.81[AFR][1000 genomes]
rs2391359	0.81[AFR][1000 genomes]
rs3801864	0.81[AFR][1000 genomes]
rs3801866	0.81[AFR][1000 genomes]
rs3801867	0.81[AFR][1000 genomes]
rs55649724	0.90[AFR][1000 genomes]
rs55959127	0.88[AFR][1000 genomes]
rs56374720	0.87[AFR][1000 genomes]
rs57579189	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57687803	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6461970	0.87[AFR][1000 genomes]
rs6943568	0.81[AFR][1000 genomes]
rs6945204	0.89[EUR][1000 genomes]
rs6967749	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970475	1.00[ASN][1000 genomes]
rs6973237	0.81[AFR][1000 genomes]
rs727449	0.92[AFR][1000 genomes]
rs73061889	0.92[AFR][1000 genomes]
rs73063604	0.88[AFR][1000 genomes]
rs73683491	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73683496	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73683510	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7777645	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780206	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782621	0.92[AFR][1000 genomes]
rs7799519	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803699	0.87[AFR][1000 genomes]
rs7809419	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9648019	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv1018125	chr7:26745074-26789814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61609910	HOXA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26731800-26779200	Weak transcription	Spleen	Spleen
2	chr7:26740400-26782400	Weak transcription	Fetal Intestine Small	intestine
3	chr7:26745000-26780800	Weak transcription	Aorta	Aorta
4	chr7:26746200-26780600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr7:26746600-26777400	Weak transcription	Lung	lung
6	chr7:26749200-26779600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr7:26749600-26781000	Weak transcription	NHEK	skin
8	chr7:26750400-26812000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:26753600-26782200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr7:26754200-26780600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr7:26754400-26782400	Weak transcription	Fetal Stomach	stomach
12	chr7:26754600-26780200	Weak transcription	NHLF	lung
13	chr7:26754800-26777000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr7:26754800-26783200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:26755600-26782400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr7:26756200-26776800	Weak transcription	Dnd41	blood
17	chr7:26756600-26780600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr7:26758400-26780800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:26763000-26777600	Weak transcription	Fetal Lung	lung
20	chr7:26763000-26780600	Weak transcription	Primary T cells from cord blood	blood
21	chr7:26763200-26776600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:26763800-26776600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr7:26763800-26780600	Weak transcription	HMEC	breast
24	chr7:26765000-26777000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr7:26765000-26778400	Weak transcription	Adipose Nuclei	Adipose
26	chr7:26766400-26776800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr7:26766600-26780600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:26767400-26780800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr7:26768800-26776200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:26770400-26780800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr7:26770600-26780400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr7:26770800-26780800	Weak transcription	GM12878-XiMat	blood
33	chr7:26772000-26780600	Weak transcription	Fetal Intestine Large	intestine
34	chr7:26772200-26780600	Weak transcription	Liver	Liver
35	chr7:26772400-26776600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr7:26773200-26780600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr7:26773400-26779600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr7:26773400-26781000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr7:26773600-26776600	Strong transcription	Primary B cells from cord blood	blood
40	chr7:26773800-26779800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr7:26773800-26780600	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr7:26774000-26779800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr7:26774000-26780600	Weak transcription	Esophagus	oesophagus
44	chr7:26774200-26776200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr7:26774600-26779200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr7:26774800-26777000	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr7:26775000-26777000	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr7:26775200-26776400	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr7:26775400-26776600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr7:26775400-26776600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

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