Variant report

Variant	rs6748435
Chromosome Location	chr2:47691120-47691121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47689406..47692258-chr2:47693990..47696937,2	K562	blood:
2	chr2:47686447..47689013-chr2:47689515..47692441,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10175959	0.91[ASN][1000 genomes]
rs10175972	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10179452	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10188090	0.93[ASN][1000 genomes]
rs10206575	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10206782	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11684661	0.93[ASN][1000 genomes]
rs11684737	0.93[ASN][1000 genomes]
rs11694689	0.89[ASN][1000 genomes]
rs11886591	0.94[ASN][1000 genomes]
rs12712993	0.82[ASN][1000 genomes]
rs12712994	0.82[ASN][1000 genomes]
rs12991125	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13031342	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1981927	0.80[ASN][1000 genomes]
rs1981928	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2059520	0.93[ASN][1000 genomes]
rs2162121	0.86[ASN][1000 genomes]
rs2347795	0.82[ASN][1000 genomes]
rs3732182	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3732183	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3764959	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3764960	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3771275	0.82[ASN][1000 genomes]
rs3771276	0.85[ASN][1000 genomes]
rs3771278	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771279	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771280	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771281	0.98[ASN][1000 genomes]
rs3821227	0.93[ASN][1000 genomes]
rs4583514	0.93[ASN][1000 genomes]
rs4596025	0.82[ASN][1000 genomes]
rs6544989	0.82[ASN][1000 genomes]
rs6544990	0.89[ASN][1000 genomes]
rs6544992	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6711675	0.96[ASN][1000 genomes]
rs6720549	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6724382	0.85[ASN][1000 genomes]
rs6724876	0.85[ASN][1000 genomes]
rs6725042	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6726691	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6726832	0.80[ASN][1000 genomes]
rs6729015	0.86[ASN][1000 genomes]
rs6737303	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6754473	0.94[ASN][1000 genomes]
rs6757035	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6758327	0.86[ASN][1000 genomes]
rs7565513	0.97[ASN][1000 genomes]
rs7585174	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7586575	0.89[ASN][1000 genomes]
rs7588420	0.89[EUR][1000 genomes]
rs7596629	0.96[ASN][1000 genomes]
rs7599880	0.82[ASN][1000 genomes]
rs7607076	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6748435	MSH2	cis	lung	GTEx
rs6748435	MSH2	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 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	chr2:47631800-47696600	Weak transcription	Esophagus	oesophagus
4	chr2:47631800-47700000	Weak transcription	Colonic Mucosa	Colon
5	chr2:47631800-47704200	Weak transcription	Psoas Muscle	Psoas
6	chr2:47633000-47714000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:47643600-47703400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:47644800-47692000	Weak transcription	Fetal Brain Male	brain
9	chr2:47658000-47707000	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:47658000-47714200	Weak transcription	Small Intestine	intestine
11	chr2:47658200-47692600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:47658200-47692600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:47658200-47709200	Weak transcription	Brain Substantia Nigra	brain
14	chr2:47658200-47710400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:47658200-47713400	Weak transcription	Fetal Heart	heart
16	chr2:47658200-47714200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:47658200-47714800	Weak transcription	HSMMtube	muscle
18	chr2:47658200-47724800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:47658400-47695200	Weak transcription	NHLF	lung
20	chr2:47658400-47713600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:47658400-47716000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:47658800-47712600	Weak transcription	Osteobl	bone
23	chr2:47661800-47692200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:47673800-47712400	Weak transcription	NHDF-Ad	bronchial
25	chr2:47674800-47696200	Weak transcription	Lung	lung
26	chr2:47677000-47710800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:47677800-47692000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:47679800-47712600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr2:47680000-47700000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr2:47681800-47692000	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:47685000-47715000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:47685400-47701200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr2:47686200-47691800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:47686400-47712600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:47686400-47712600	Strong transcription	Dnd41	blood
36	chr2:47687000-47692000	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr2:47687200-47706800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:47688200-47698200	Weak transcription	HUVEC	blood vessel
39	chr2:47688600-47703000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr2:47689000-47692000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:47689200-47713000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:47689400-47694400	Strong transcription	HepG2	liver
43	chr2:47689400-47700800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:47689400-47703000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:47689400-47712800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:47689800-47691800	Strong transcription	Brain Germinal Matrix	brain
47	chr2:47689800-47694200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:47689800-47700200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:47689800-47713000	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr2:47690000-47691200	Strong transcription	NH-A	brain

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