Variant report

Variant	rs540866
Chromosome Location	chr11:100833059-100833060
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	chr11:100828736..100830858-chr11:100832178..100833862,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165895	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10501968	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs10791431	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10791440	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11224507	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11224509	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11224526	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs11224530	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs1145434	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11534487	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12416898	0.91[ASN][1000 genomes]
rs12417055	0.86[ASN][1000 genomes]
rs12417065	0.86[ASN][1000 genomes]
rs12417366	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs12417367	1.00[CHB][hapmap];0.84[JPT][hapmap];0.96[ASN][1000 genomes]
rs12417750	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12417981	0.90[ASN][1000 genomes]
rs12418060	0.87[ASN][1000 genomes]
rs12418330	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs12418450	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs12418561	0.96[ASN][1000 genomes]
rs12418769	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs12419150	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs12419214	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12419257	0.94[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs12420084	0.96[ASN][1000 genomes]
rs12420453	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs12420466	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs12420698	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs12420922	0.91[ASN][1000 genomes]
rs12421386	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12421655	0.86[ASN][1000 genomes]
rs12422140	1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs17095808	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs17095820	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs17095829	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs1893683	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1940221	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1943499	0.86[ASN][1000 genomes]
rs1943500	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1944432	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs1944433	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs1944434	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs2155444	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs2155445	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs2165664	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2165665	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2186784	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2186785	0.88[CHB][hapmap];0.96[ASN][1000 genomes]
rs2186786	0.94[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs2277274	0.98[ASN][1000 genomes]
rs2277275	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs2407822	0.85[ASN][1000 genomes]
rs2407823	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2407825	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28492796	0.91[ASN][1000 genomes]
rs2897779	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3843607	0.86[ASN][1000 genomes]
rs3886266	0.86[ASN][1000 genomes]
rs4587692	0.85[ASN][1000 genomes]
rs471933	0.92[MEX][hapmap]
rs473765	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs475432	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs4754708	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4754709	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs479135	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs480145	0.96[ASN][1000 genomes]
rs485269	0.94[CEU][hapmap];0.83[CHB][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs497234	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs501831	0.96[ASN][1000 genomes]
rs505458	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs507858	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs515868	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs516873	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527433	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs527689	0.86[ASN][1000 genomes]
rs533384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs533571	0.91[GIH][hapmap]
rs535747	1.00[CEU][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs539648	0.91[ASN][1000 genomes]
rs543146	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs549510	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs551632	0.82[GIH][hapmap]
rs552490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs554077	0.96[ASN][1000 genomes]
rs555825	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs55745131	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56320976	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs563460	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs568618	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569336	0.80[CEU][hapmap];0.84[AFR][1000 genomes]
rs57502383	0.95[ASN][1000 genomes]
rs575734	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs576472	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs583415	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs590616	0.91[GIH][hapmap]
rs601016	0.96[ASN][1000 genomes]
rs60423120	1.00[ASN][1000 genomes]
rs60612076	0.96[ASN][1000 genomes]
rs623072	0.86[ASN][1000 genomes]
rs626529	0.91[ASN][1000 genomes]
rs631172	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs634968	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs640326	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs647256	0.86[ASN][1000 genomes]
rs658497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659034	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6590829	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs6590830	1.00[ASN][1000 genomes]
rs6590831	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs6590832	0.97[ASN][1000 genomes]
rs6590833	1.00[ASN][1000 genomes]
rs661973	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs662453	0.84[ASN][1000 genomes]
rs668513	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs688146	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7110858	1.00[ASN][1000 genomes]
rs7114062	0.94[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs7130581	1.00[ASN][1000 genomes]
rs7130586	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs7933033	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs7950572	1.00[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	nsv1048356	chr11:100713096-101058995	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv541154	chr11:100713096-101058995	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs540866	TMEM133	cis	lymphoblastoid	seeQTL
rs540866	DYNC2H1	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100785400-100838400	Weak transcription	Fetal Intestine Small	intestine
2	chr11:100800200-100846600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:100800800-100835800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr11:100801000-100835000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr11:100801400-100833800	Weak transcription	NH-A	brain
6	chr11:100806600-100837200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:100807800-100844600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr11:100808000-100846600	Weak transcription	Ovary	ovary
9	chr11:100810000-100852200	Weak transcription	Small Intestine	intestine
10	chr11:100810400-100845000	Weak transcription	Primary B cells from cord blood	blood
11	chr11:100810600-100848400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr11:100812000-100841000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:100813000-100848600	Weak transcription	A549	lung
14	chr11:100813200-100838800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:100813200-100841400	Weak transcription	Fetal Stomach	stomach
16	chr11:100813200-100846600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr11:100813400-100834800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr11:100813800-100834000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr11:100814200-100835600	Weak transcription	Dnd41	blood
20	chr11:100820400-100841400	Weak transcription	Right Ventricle	heart
21	chr11:100820400-100847000	Weak transcription	Fetal Kidney	kidney
22	chr11:100823800-100833600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr11:100827200-100840200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr11:100827400-100846600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr11:100827600-100835000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:100828400-100845400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr11:100828600-100846400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr11:100828800-100849400	Weak transcription	NHLF	lung
29	chr11:100829000-100849400	Weak transcription	HMEC	breast
30	chr11:100829200-100834400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr11:100829200-100846800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr11:100829600-100833800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr11:100829600-100833800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:100829600-100841400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr11:100829600-100849400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr11:100830000-100847600	Weak transcription	Psoas Muscle	Psoas
37	chr11:100830200-100838000	Strong transcription	Placenta	Placenta
38	chr11:100830400-100839000	Strong transcription	Liver	Liver
39	chr11:100830600-100834800	Weak transcription	Fetal Heart	heart
40	chr11:100830600-100858200	Weak transcription	Colonic Mucosa	Colon
41	chr11:100831200-100836400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr11:100831200-100837000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr11:100831400-100836400	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr11:100831600-100834400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:100831800-100834200	Strong transcription	Left Ventricle	heart
46	chr11:100831800-100834200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr11:100831800-100835800	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr11:100831800-100836600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:100832000-100833800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr11:100832000-100834200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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