Variant report

Variant	rs10240542
Chromosome Location	chr7:66533356-66533357
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10081382	1.00[ASN][1000 genomes]
rs10243730	1.00[ASN][1000 genomes]
rs10247355	1.00[ASN][1000 genomes]
rs10264939	1.00[ASN][1000 genomes]
rs10266985	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13222551	1.00[ASN][1000 genomes]
rs13222852	1.00[ASN][1000 genomes]
rs13222880	1.00[ASN][1000 genomes]
rs13222968	0.81[AFR][1000 genomes]
rs13239441	1.00[ASN][1000 genomes]
rs13241749	1.00[ASN][1000 genomes]
rs13246453	1.00[ASN][1000 genomes]
rs2421427	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28524910	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28828435	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28875922	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901443	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34208798	0.83[AFR][1000 genomes]
rs35175278	1.00[ASN][1000 genomes]
rs35955950	1.00[ASN][1000 genomes]
rs3980714	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3980761	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56042635	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56081654	1.00[ASN][1000 genomes]
rs56224758	1.00[ASN][1000 genomes]
rs56259510	1.00[ASN][1000 genomes]
rs56376467	1.00[ASN][1000 genomes]
rs57571665	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59540627	0.80[AFR][1000 genomes]
rs66701377	1.00[ASN][1000 genomes]
rs6948594	0.82[EUR][1000 genomes]
rs6956400	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958056	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6968898	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6973163	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73144570	1.00[ASN][1000 genomes]
rs73381658	0.84[AFR][1000 genomes]
rs7780458	0.82[YRI][hapmap]
rs7783776	1.00[ASN][1000 genomes]
rs7789673	1.00[ASN][1000 genomes]
rs7791848	1.00[ASN][1000 genomes]
rs7795025	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7797194	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809602	1.00[ASN][1000 genomes]
rs7811073	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9654770	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9691420	1.00[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	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1032575	chr7:66432853-66576034	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	nsv831019	chr7:66516808-66720485	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10240542	TYW1	cis	Muscle Skeletal	GTEx
rs10240542	TYW1	cis	Esophagus Mucosa	GTEx
rs10240542	TYW1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66483400-66551200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:66483600-66534400	Weak transcription	Aorta	Aorta
3	chr7:66487000-66576600	Weak transcription	Gastric	stomach
4	chr7:66495200-66538000	Weak transcription	Brain Germinal Matrix	brain
5	chr7:66495200-66539400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr7:66495200-66597200	Weak transcription	Right Ventricle	heart
7	chr7:66495400-66534400	Weak transcription	Spleen	Spleen
8	chr7:66495600-66547400	Weak transcription	Pancreas	Pancrea
9	chr7:66498600-66534600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:66498600-66549400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr7:66501000-66540000	Weak transcription	Psoas Muscle	Psoas
12	chr7:66502400-66534400	Weak transcription	Lung	lung
13	chr7:66502400-66549600	Weak transcription	Brain Hippocampus Middle	brain
14	chr7:66506600-66534600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr7:66508000-66533400	Weak transcription	Colon Smooth Muscle	Colon
16	chr7:66508800-66533400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr7:66508800-66533800	Weak transcription	Hela-S3	cervix
18	chr7:66508800-66537600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr7:66508800-66538000	Weak transcription	A549	lung
20	chr7:66508800-66590400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:66509000-66538000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr7:66509000-66539600	Weak transcription	HMEC	breast
23	chr7:66509400-66536600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr7:66511200-66537600	Weak transcription	Brain Substantia Nigra	brain
25	chr7:66511400-66539800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:66512400-66535000	Weak transcription	Colonic Mucosa	Colon
27	chr7:66512400-66540600	Weak transcription	HepG2	liver
28	chr7:66515600-66537600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr7:66515600-66538000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr7:66516200-66534400	Weak transcription	Placenta	Placenta
31	chr7:66516400-66534600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr7:66516400-66551600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr7:66516800-66540200	Weak transcription	Fetal Brain Female	brain
34	chr7:66517000-66533800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr7:66518400-66574200	Weak transcription	Small Intestine	intestine
36	chr7:66519200-66539800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr7:66519600-66543400	Weak transcription	Fetal Brain Male	brain
38	chr7:66521800-66538000	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr7:66523400-66541000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr7:66523600-66541000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr7:66523800-66533800	Weak transcription	Fetal Muscle Leg	muscle
42	chr7:66523800-66534400	Weak transcription	Esophagus	oesophagus
43	chr7:66525600-66534400	Weak transcription	Fetal Stomach	stomach
44	chr7:66526400-66585600	Weak transcription	Brain Angular Gyrus	brain
45	chr7:66527000-66540600	Weak transcription	HUVEC	blood vessel
46	chr7:66527600-66539600	Weak transcription	NHEK	skin
47	chr7:66528000-66537800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr7:66528800-66536600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr7:66529000-66534400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr7:66529000-66534400	Weak transcription	Fetal Intestine Small	intestine

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