Variant report

Variant	rs7696306
Chromosome Location	chr4:8389187-8389188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10016221	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.95[ASN][1000 genomes]
rs10017177	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1006113	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938710	0.87[ASN][1000 genomes]
rs10938712	0.97[ASN][1000 genomes]
rs11721377	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11724408	0.96[ASN][1000 genomes]
rs11731308	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11931965	0.98[ASN][1000 genomes]
rs11934603	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11938364	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.98[ASN][1000 genomes]
rs13103946	0.96[ASN][1000 genomes]
rs13107329	0.96[ASN][1000 genomes]
rs13130336	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13134272	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13136987	0.92[ASW][hapmap];0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13139522	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13150818	0.95[ASN][1000 genomes]
rs1568692	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1568693	0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs2242483	0.93[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2293229	0.92[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs2386119	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap]
rs28637781	0.98[ASN][1000 genomes]
rs28805000	0.96[ASN][1000 genomes]
rs34947973	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35893558	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796740	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs4543095	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6447868	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs73087705	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7668735	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291391	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9291392	0.98[ASN][1000 genomes]
rs950306	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878595	chr4:8154534-8390646	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv461219	chr4:8353829-8390646	Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv593637	chr4:8353829-8390646	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv878609	chr4:8373832-8407406	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv878610	chr4:8377058-8416976	ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
14	esv1005399	chr4:8387281-8397983	Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7696306	RP11-689P11.2	cis	Artery Tibial	GTEx
rs7696306	C4orf23	cis	parietal	SCAN
rs7696306	PPP2R2C	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8360400-8394000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:8360400-8395600	Weak transcription	NHEK	skin
3	chr4:8362000-8395400	Weak transcription	Fetal Brain Male	brain
4	chr4:8364800-8392400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:8366400-8411600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:8366800-8390000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr4:8372600-8389800	Strong transcription	Esophagus	oesophagus
8	chr4:8373400-8401600	Strong transcription	Fetal Intestine Small	intestine
9	chr4:8375000-8401600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:8378000-8391800	Strong transcription	Fetal Brain Female	brain
11	chr4:8378600-8398600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:8378600-8398800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr4:8378800-8397800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:8379000-8395400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:8379400-8392000	Strong transcription	Brain Hippocampus Middle	brain
16	chr4:8381000-8393800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:8381600-8392400	Strong transcription	Brain Cingulate Gyrus	brain
18	chr4:8381800-8394400	Strong transcription	Brain Germinal Matrix	brain
19	chr4:8381800-8398600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr4:8382400-8401600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:8383800-8419000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr4:8384000-8394600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:8384000-8395600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:8384000-8399600	Strong transcription	Spleen	Spleen
25	chr4:8384800-8390000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:8384800-8391000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:8384800-8392000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr4:8384800-8401600	Strong transcription	Thymus	Thymus
29	chr4:8384800-8418600	Strong transcription	Primary T cells from cord blood	blood
30	chr4:8385200-8395200	Weak transcription	Fetal Kidney	kidney
31	chr4:8385200-8411600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr4:8385400-8395600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:8385600-8392400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr4:8385600-8407000	Weak transcription	Stomach Mucosa	stomach
35	chr4:8385800-8391200	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr4:8386000-8389800	Weak transcription	NH-A	brain
37	chr4:8386000-8393400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:8386200-8391400	Strong transcription	Brain Angular Gyrus	brain
39	chr4:8386200-8392200	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr4:8386400-8391400	Strong transcription	Gastric	stomach
41	chr4:8386400-8392400	Weak transcription	GM12878-XiMat	blood
42	chr4:8386400-8393000	Strong transcription	Fetal Stomach	stomach
43	chr4:8386400-8398200	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr4:8386400-8408400	Strong transcription	Fetal Intestine Large	intestine
45	chr4:8386600-8390000	Weak transcription	HSMM	muscle
46	chr4:8386600-8393400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:8386600-8398600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr4:8386600-8399400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr4:8386600-8400600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:8386800-8391800	Strong transcription	Primary B cells from cord blood	blood

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