Variant report

Variant	rs6753135
Chromosome Location	chr2:47657684-47657685
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12615967	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17036577	1.00[ASN][1000 genomes]
rs17217989	1.00[ASN][1000 genomes]
rs17224388	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58064086	1.00[ASN][1000 genomes]
rs62139717	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62139718	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72884648	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72884696	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv527823	chr2:47645249-47709704	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6753135	RHOQ	cis	parietal	SCAN
rs6753135	MSH2	cis	cerebellum	SCAN
rs6753135	DYNC2LI1	cis	cerebellum	SCAN
rs6753135	ABCG8	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47631400-47697000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:47631400-47714400	Weak transcription	Right Ventricle	heart
3	chr2:47631800-47659400	Weak transcription	Right Atrium	heart
4	chr2:47631800-47672000	Weak transcription	Pancreas	Pancrea
5	chr2:47631800-47696600	Weak transcription	Esophagus	oesophagus
6	chr2:47631800-47700000	Weak transcription	Colonic Mucosa	Colon
7	chr2:47631800-47704200	Weak transcription	Psoas Muscle	Psoas
8	chr2:47632600-47659600	Strong transcription	Fetal Thymus	thymus
9	chr2:47632800-47659600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr2:47633000-47659600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:47633000-47659600	Strong transcription	Fetal Stomach	stomach
12	chr2:47633000-47714000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:47634600-47657800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:47634800-47658800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:47634800-47659600	Strong transcription	Dnd41	blood
16	chr2:47635600-47657800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:47636800-47659600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:47637600-47658000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:47643600-47703400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:47644800-47692000	Weak transcription	Fetal Brain Male	brain
21	chr2:47647400-47662800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:47648600-47668600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:47649200-47659600	Strong transcription	Thymus	Thymus
24	chr2:47652000-47666400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:47652800-47658400	Strong transcription	Primary T cells from cord blood	blood
26	chr2:47654000-47659200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:47655200-47659600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:47655600-47659600	Strong transcription	HepG2	liver
29	chr2:47655600-47682800	Weak transcription	Stomach Mucosa	stomach
30	chr2:47656000-47659600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:47656200-47657800	Strong transcription	Fetal Intestine Small	intestine
32	chr2:47656400-47657800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr2:47656400-47658400	Strong transcription	Placenta	Placenta
34	chr2:47656400-47659400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:47656400-47659600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:47656400-47659600	Strong transcription	Fetal Muscle Leg	muscle
37	chr2:47656600-47658200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:47656600-47658400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr2:47656600-47659400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:47656600-47659600	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr2:47656800-47658000	Genic enhancers	NHEK	skin
42	chr2:47656800-47659600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:47657000-47658000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr2:47657000-47658200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr2:47657000-47658200	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr2:47657000-47658200	Strong transcription	HMEC	breast
47	chr2:47657000-47658400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr2:47657000-47658400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr2:47657000-47658400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr2:47657000-47658400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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