Variant report

Variant	rs17095429
Chromosome Location	chr11:100639302-100639303
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs17095405	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17095409	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17095426	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17095428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17095438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17095439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088953	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2407750	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3901516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4087602	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4121392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4337001	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4469852	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4517481	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4754702	0.81[ASW][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap]
rs499241	0.81[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs507695	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs58727919	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60708905	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61890760	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61890763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61890764	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61890765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61890766	1.00[ASN][1000 genomes]
rs61892334	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61892352	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61892355	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61910508	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6590818	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7102634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7105842	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7110872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7112228	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7112366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7116153	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7117515	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7120712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7126324	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7130855	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73005729	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7927197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7942588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7944598	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7947761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520995	chr11:100163957-100681211	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv530643	chr11:100196082-100713156	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17095429	TMEM123	cis	cerebellum	SCAN
rs17095429	TMEM133	cis	parietal	SCAN
rs17095429	TMEM133	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100621000-100642400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr11:100624600-100655600	Weak transcription	Left Ventricle	heart
3	chr11:100624600-100655600	Weak transcription	Right Ventricle	heart
4	chr11:100626000-100639600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr11:100628200-100642800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr11:100629200-100642800	Weak transcription	Liver	Liver
7	chr11:100631000-100639600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr11:100631800-100645000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:100632000-100640000	Weak transcription	Fetal Heart	heart
10	chr11:100632200-100640000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:100632200-100645200	Weak transcription	Colonic Mucosa	Colon
12	chr11:100632200-100647200	Weak transcription	HSMM	muscle
13	chr11:100632800-100639600	Weak transcription	Fetal Lung	lung
14	chr11:100632800-100645000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr11:100632800-100645000	Weak transcription	Gastric	stomach
16	chr11:100633000-100641600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:100633000-100647000	Weak transcription	NHLF	lung
18	chr11:100633200-100639800	Weak transcription	Adipose Nuclei	Adipose
19	chr11:100633200-100641800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:100633200-100641800	Weak transcription	Fetal Muscle Leg	muscle
21	chr11:100633200-100642600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr11:100633200-100655600	Weak transcription	Psoas Muscle	Psoas
23	chr11:100633600-100647400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr11:100635200-100639600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:100635200-100647400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr11:100635400-100649400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr11:100635600-100639600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr11:100635800-100639600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr11:100635800-100645600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr11:100636000-100639600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr11:100636600-100639600	Weak transcription	Stomach Mucosa	stomach
32	chr11:100636600-100643000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr11:100637000-100639600	Weak transcription	Fetal Intestine Small	intestine
34	chr11:100637000-100644400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr11:100637400-100640200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr11:100638000-100639800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:100638400-100639800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr11:100638400-100641200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:100638600-100640200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr11:100638600-100641400	Weak transcription	Placenta	Placenta
41	chr11:100638800-100639400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr11:100639000-100640800	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr11:100639000-100640800	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr11:100639200-100639800	Weak transcription	Small Intestine	intestine
45	chr11:100639200-100640800	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr11:100639200-100640800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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