Variant report

Variant	rs7589162
Chromosome Location	chr2:39053545-39053546
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39036853..39041014-chr2:39051745..39054794,3	K562	blood:
2	chr2:39053503..39057037-chr2:39058758..39062643,3	K562	blood:
3	chr2:39052271..39054519-chr2:39105359..39107014,2	K562	blood:
4	chr2:38976908..38981867-chr2:39050395..39056507,16	K562	blood:
5	chr2:38970642..38974334-chr2:39052366..39056279,4	K562	blood:
6	chr2:39053503..39055563-chr2:39060007..39062643,2	K562	blood:

Variant related genes	Relation type
ENSG00000223922	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10168789	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10173118	0.81[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10173240	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10176932	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10779923	0.86[JPT][hapmap]
rs10865143	0.81[CEU][hapmap]
rs10865144	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11124646	0.88[CHB][hapmap]
rs11694383	0.94[CHB][hapmap];0.84[EUR][1000 genomes]
rs11889280	0.82[EUR][1000 genomes]
rs12465043	0.86[ASN][1000 genomes]
rs12465365	0.82[ASN][1000 genomes]
rs12468732	0.80[ASN][1000 genomes]
rs12469681	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12473036	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12477252	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12623330	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12712621	0.80[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12712622	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12712624	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12712625	0.85[CEU][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap]
rs12712627	0.85[CEU][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap]
rs12996194	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13011522	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13014136	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13029388	0.82[CEU][hapmap];0.81[YRI][hapmap]
rs13029406	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13383541	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13411868	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13417196	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1530852	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1530853	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1901289	0.86[YRI][hapmap]
rs1979142	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1997377	0.81[CHB][hapmap]
rs2272445	0.88[CHB][hapmap]
rs3099940	0.81[CHB][hapmap]
rs3099965	0.86[EUR][1000 genomes]
rs3099984	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3099985	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3099987	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099988	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099989	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099991	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3112140	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3112149	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112159	0.81[CEU][hapmap]
rs3112200	0.81[CEU][hapmap];0.94[CHB][hapmap];0.81[EUR][1000 genomes]
rs3112205	0.84[EUR][1000 genomes]
rs3112210	0.86[EUR][1000 genomes]
rs3112215	0.94[CHB][hapmap]
rs3112216	0.84[EUR][1000 genomes]
rs373300	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs3770681	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4265996	0.87[JPT][hapmap];0.80[YRI][hapmap]
rs4602206	0.82[CEU][hapmap];0.94[CHB][hapmap]
rs4630748	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs4670894	0.83[ASN][1000 genomes]
rs4670897	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56393601	0.83[EUR][1000 genomes]
rs60012208	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715866	0.81[CEU][hapmap]
rs6723868	0.95[ASN][1000 genomes]
rs6728394	0.88[CHB][hapmap]
rs6746818	0.82[CEU][hapmap]
rs6753251	0.83[EUR][1000 genomes]
rs6756847	0.88[CHB][hapmap]
rs7419616	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7419838	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7565111	0.86[JPT][hapmap]
rs7588621	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7591959	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7598922	0.81[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs7602287	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7603676	0.88[CHB][hapmap]
rs9808136	0.84[YRI][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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7589162	SFRS7	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:39019000-39057800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:39022000-39066800	Weak transcription	Stomach Mucosa	stomach
4	chr2:39026600-39079800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
6	chr2:39032800-39072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:39036000-39054000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:39037200-39055800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:39037400-39054000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:39037400-39054000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr2:39037400-39054600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:39037800-39053800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:39038200-39056000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:39038800-39102200	Weak transcription	Gastric	stomach
16	chr2:39039000-39085400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:39039000-39090000	Weak transcription	Esophagus	oesophagus
18	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
20	chr2:39040000-39069000	Strong transcription	Fetal Muscle Leg	muscle
21	chr2:39040600-39056000	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:39040800-39054200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:39042800-39063000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:39042800-39080600	Weak transcription	Small Intestine	intestine
25	chr2:39043600-39079800	Weak transcription	Right Ventricle	heart
26	chr2:39043800-39053800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:39044800-39056800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr2:39046000-39073200	Weak transcription	Pancreas	Pancrea
29	chr2:39046200-39070200	Weak transcription	NHLF	lung
30	chr2:39046400-39057200	Weak transcription	HepG2	liver
31	chr2:39048000-39055600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:39048400-39054200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:39048400-39060800	Strong transcription	Fetal Stomach	stomach
34	chr2:39049000-39054400	Strong transcription	Placenta	Placenta
35	chr2:39049000-39056000	Strong transcription	Fetal Intestine Small	intestine
36	chr2:39049200-39053800	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:39049400-39053800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:39049400-39053800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:39049400-39054000	Strong transcription	Brain Hippocampus Middle	brain
40	chr2:39049400-39054200	Strong transcription	Fetal Brain Female	brain
41	chr2:39049400-39054800	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:39049400-39055400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:39049600-39053600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:39049600-39053600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:39049600-39053800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:39049600-39053800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:39049600-39053800	Strong transcription	Adipose Nuclei	Adipose
48	chr2:39049600-39053800	Strong transcription	Fetal Lung	lung
49	chr2:39049600-39053800	Strong transcription	Stomach Smooth Muscle	stomach
50	chr2:39049600-39054000	Strong transcription	H1 Cell Line	embryonic stem cell

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