Variant report

Variant	rs16842845
Chromosome Location	chr3:100509475-100509476
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	chr3:100480324..100483871-chr3:100505930..100509875,3	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1048364	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap]
rs11716316	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12496951	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13078643	0.89[CEU][hapmap]
rs13086822	0.89[CEU][hapmap]
rs1503839	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503845	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1520649	0.89[CEU][hapmap];0.84[GIH][hapmap]
rs1553455	0.81[CEU][hapmap];0.80[AMR][1000 genomes]
rs16842822	0.87[CHD][hapmap]
rs1847391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1994085	0.89[CEU][hapmap]
rs2055543	0.89[CEU][hapmap];0.88[MEX][hapmap]
rs2169553	0.80[CEU][hapmap]
rs2293030	0.89[CEU][hapmap]
rs34281646	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35734168	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3736534	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3773921	0.89[CEU][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap]
rs3862285	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4616685	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4928083	0.89[CEU][hapmap];0.88[MEX][hapmap]
rs4928085	0.83[CEU][hapmap];0.84[GIH][hapmap];0.80[MEX][hapmap]
rs4928086	0.89[CEU][hapmap]
rs544500	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs547330	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs58758917	0.87[ASN][1000 genomes]
rs754462	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7609779	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs7612334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7613610	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs7632038	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs7642598	0.89[CEU][hapmap]
rs7642942	0.90[CHD][hapmap]
rs764684	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs900233	0.89[CEU][hapmap]
rs971230	0.87[CEU][hapmap]
rs9824346	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs983474	0.82[JPT][hapmap]
rs9842968	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs9850273	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs989793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs989794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs989795	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796184	chr3:100507827-100522384	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16842845	C14orf21	trans	cerebellum	SCAN
rs16842845	IMPG2	cis	cerebellum	SCAN
rs16842845	TFG	Cis_1M	lymphoblastoid	RTeQTL
rs16842845	CBLB	cis	parietal	SCAN
rs16842845	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100475600-100520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:100494800-100523400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:100496800-100511200	Weak transcription	Aorta	Aorta
4	chr3:100501200-100516600	Weak transcription	HSMM	muscle
5	chr3:100502200-100518600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:100502400-100530400	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:100502600-100516800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:100505000-100510400	Weak transcription	Psoas Muscle	Psoas
9	chr3:100505000-100515400	Weak transcription	Adipose Nuclei	Adipose
10	chr3:100505000-100515400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:100505000-100516600	Weak transcription	Left Ventricle	heart
12	chr3:100505200-100510800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:100505200-100512800	Weak transcription	HSMMtube	muscle
14	chr3:100505200-100515200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:100505200-100515200	Weak transcription	Fetal Stomach	stomach
16	chr3:100505200-100515400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:100505200-100515400	Weak transcription	HUVEC	blood vessel
18	chr3:100505200-100558200	Weak transcription	Ovary	ovary
19	chr3:100505200-100582800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:100505600-100514400	Strong transcription	Osteobl	bone
21	chr3:100505800-100515400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:100505800-100515400	Weak transcription	Fetal Lung	lung
23	chr3:100506000-100548400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:100507000-100515400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:100509000-100512600	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:100509200-100515400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:100509200-100515400	Weak transcription	NHDF-Ad	bronchial
28	chr3:100509200-100518200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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