Variant report

Variant	rs7633687
Chromosome Location	chr3:52382822-52382823
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52332184..52333730-chr3:52381219..52384189,2	K562	blood:

Variant related genes	Relation type
ENSG00000242797	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10460962	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs10461027	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10461028	0.91[EUR][1000 genomes]
rs10865971	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11706515	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11706541	0.87[EUR][1000 genomes]
rs11707056	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11708581	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11708811	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11710014	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs11711914	0.88[EUR][1000 genomes]
rs11711974	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11713914	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11714358	0.94[EUR][1000 genomes]
rs11715208	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11715382	0.86[EUR][1000 genomes]
rs11715391	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs11716487	1.00[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs11717028	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11718729	0.90[EUR][1000 genomes]
rs11719760	0.87[EUR][1000 genomes]
rs11720365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11721277	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17052051	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17052052	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs17052053	0.91[CEU][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs17052054	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17263770	1.00[CEU][hapmap];0.81[YRI][hapmap];0.87[EUR][1000 genomes]
rs1767	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs1769	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs35976326	0.94[EUR][1000 genomes]
rs3733063	0.91[CEU][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs3886875	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4082828	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs55676974	0.94[EUR][1000 genomes]
rs55806905	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55813842	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55847657	0.90[EUR][1000 genomes]
rs56002041	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56322342	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56352611	0.90[EUR][1000 genomes]
rs56899118	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57849650	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58531656	0.90[EUR][1000 genomes]
rs60382084	0.90[EUR][1000 genomes]
rs61644644	0.94[EUR][1000 genomes]
rs6445385	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6776759	0.87[EUR][1000 genomes]
rs6783652	0.94[EUR][1000 genomes]
rs6793317	0.91[CEU][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs6809248	0.90[EUR][1000 genomes]
rs724801	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs729555	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73072990	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73088773	0.91[EUR][1000 genomes]
rs73088783	0.90[EUR][1000 genomes]
rs73088785	0.90[EUR][1000 genomes]
rs73088791	0.94[EUR][1000 genomes]
rs73088800	0.90[EUR][1000 genomes]
rs73091166	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091168	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs746239	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7615405	0.97[EUR][1000 genomes]
rs7628461	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs7638204	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs7643913	0.86[CEU][hapmap];0.94[EUR][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	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
2	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
4	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7633687	TKT	cis	cerebellum	SCAN
rs7633687	LOC286359	trans	parietal	SCAN
rs7633687	DNAH1	cis	parietal	SCAN
rs7633687	SEMA3G	cis	cerebellum	SCAN
rs7633687	NISCH	cis	lymphoblastoid	seeQTL
rs7633687	PPM1M	cis	parietal	SCAN
rs7633687	NISCH	cis	parietal	SCAN
rs7633687	DNAH1	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52352200-52384600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:52354800-52384000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:52364200-52383000	Weak transcription	Fetal Lung	lung
4	chr3:52364800-52394400	Weak transcription	HSMMtube	muscle
5	chr3:52366400-52383000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:52366600-52386600	Weak transcription	Aorta	Aorta
7	chr3:52366800-52383000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:52367600-52384400	Weak transcription	Fetal Kidney	kidney
9	chr3:52368400-52383000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:52373800-52396000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:52374000-52385400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:52374000-52386200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:52374000-52399000	Weak transcription	Stomach Mucosa	stomach
14	chr3:52374000-52407000	Strong transcription	Fetal Intestine Small	intestine
15	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:52375400-52405600	Strong transcription	Lung	lung
17	chr3:52376400-52402000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:52376800-52384400	Weak transcription	GM12878-XiMat	blood
19	chr3:52377000-52406600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:52377000-52406600	Strong transcription	Liver	Liver
21	chr3:52377200-52390600	Strong transcription	Primary T cells from cord blood	blood
22	chr3:52377200-52405200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr3:52377400-52384600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr3:52377400-52397400	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr3:52377400-52404800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:52377400-52406600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:52377400-52406800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:52377600-52384000	Weak transcription	Fetal Thymus	thymus
29	chr3:52377600-52406200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:52377800-52384400	Strong transcription	Spleen	Spleen
31	chr3:52377800-52406200	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr3:52377800-52407200	Strong transcription	Fetal Intestine Large	intestine
33	chr3:52378200-52391600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr3:52378400-52400000	Strong transcription	Brain Anterior Caudate	brain
35	chr3:52378400-52401200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:52378400-52401200	Strong transcription	Gastric	stomach
37	chr3:52378400-52401800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:52378600-52384400	Strong transcription	Brain Angular Gyrus	brain
39	chr3:52378600-52389800	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:52378600-52390800	Strong transcription	Thymus	Thymus
41	chr3:52378600-52400000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:52378600-52400200	Strong transcription	Brain Cingulate Gyrus	brain
43	chr3:52378600-52400200	Strong transcription	Brain Hippocampus Middle	brain
44	chr3:52378600-52405000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:52378600-52406800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:52379200-52389800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:52379200-52391000	Strong transcription	Primary B cells from cord blood	blood
48	chr3:52379400-52383200	Genic enhancers	Pancreas	Pancrea
49	chr3:52379400-52410600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr3:52380000-52383000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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