Variant report

Variant	rs2041672
Chromosome Location	chr4:15552295-15552296
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1154577	0.84[ASN][1000 genomes]
rs11726647	0.86[JPT][hapmap]
rs13106528	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13114491	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13122812	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13127507	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13131119	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13131285	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13131606	0.81[ASN][1000 genomes]
rs13138894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13141724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13144428	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468735	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468736	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16892135	1.00[JPT][hapmap]
rs16892143	1.00[ASW][hapmap];1.00[CEU][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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16892156	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17476670	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17476831	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1786	0.86[JPT][hapmap]
rs2041673	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3182730	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34155734	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34427409	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34599140	1.00[ASN][1000 genomes]
rs34831330	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34924677	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35151159	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35196224	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35258636	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35309200	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35461787	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35724720	0.84[ASN][1000 genomes]
rs36012186	0.84[ASN][1000 genomes]
rs3756247	0.86[JPT][hapmap]
rs41417147	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4267734	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4301111	0.86[JPT][hapmap]
rs4326008	1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4396986	0.86[JPT][hapmap]
rs4423870	0.86[JPT][hapmap]
rs4549375	0.86[JPT][hapmap]
rs4613560	1.00[ASN][1000 genomes]
rs57275698	0.84[ASN][1000 genomes]
rs6414764	0.86[JPT][hapmap]
rs6449150	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66472670	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67047740	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67089836	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67222859	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67224550	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815254	0.86[JPT][hapmap]
rs6824422	0.86[JPT][hapmap]
rs6825051	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825815	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6826058	0.86[JPT][hapmap]
rs6834359	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835038	1.00[JPT][hapmap]
rs6839654	0.86[JPT][hapmap]
rs6844141	1.00[JPT][hapmap]
rs6852735	0.85[JPT][hapmap]
rs73237149	0.84[ASN][1000 genomes]
rs73237151	0.84[ASN][1000 genomes]
rs7699180	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2041672	C1QTNF7	cis	cerebellum	SCAN
rs2041672	FAM200B	cis	parietal	SCAN
rs2041672	LOC285550	cis	multi-tissue	Pritchard

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15487400-15570400	Weak transcription	Psoas Muscle	Psoas
2	chr4:15495600-15559400	Weak transcription	HSMMtube	muscle
3	chr4:15502800-15577600	Weak transcription	Right Ventricle	heart
4	chr4:15508200-15556400	Weak transcription	Colonic Mucosa	Colon
5	chr4:15509200-15564400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:15509600-15553400	Weak transcription	HepG2	liver
7	chr4:15512000-15580000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:15513000-15562400	Weak transcription	Primary B cells from cord blood	blood
9	chr4:15517800-15593600	Weak transcription	HUVEC	blood vessel
10	chr4:15520000-15572400	Weak transcription	Small Intestine	intestine
11	chr4:15520600-15553400	Weak transcription	A549	lung
12	chr4:15526000-15558200	Weak transcription	Spleen	Spleen
13	chr4:15530200-15556600	Weak transcription	HSMM	muscle
14	chr4:15530800-15554600	Weak transcription	Placenta	Placenta
15	chr4:15530800-15554600	Weak transcription	NH-A	brain
16	chr4:15533000-15554800	Weak transcription	Fetal Brain Male	brain
17	chr4:15537200-15565000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
19	chr4:15539000-15570400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr4:15540000-15555600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:15540200-15554400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr4:15540200-15554600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:15540200-15555400	Weak transcription	NHLF	lung
24	chr4:15540200-15556800	Weak transcription	Brain Hippocampus Middle	brain
25	chr4:15540200-15558200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:15540200-15558200	Weak transcription	Brain Angular Gyrus	brain
27	chr4:15540200-15558200	Weak transcription	Brain Anterior Caudate	brain
28	chr4:15540200-15559600	Weak transcription	Esophagus	oesophagus
29	chr4:15540200-15561600	Weak transcription	HMEC	breast
30	chr4:15540200-15561600	Weak transcription	NHEK	skin
31	chr4:15540200-15562600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:15540400-15554600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr4:15540400-15563200	Weak transcription	Brain Substantia Nigra	brain
34	chr4:15540400-15565000	Weak transcription	NHDF-Ad	bronchial
35	chr4:15541600-15554600	Weak transcription	Osteobl	bone
36	chr4:15542600-15554200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:15543800-15570600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr4:15544000-15553800	Weak transcription	Fetal Kidney	kidney
39	chr4:15544400-15553400	Weak transcription	Fetal Intestine Large	intestine
40	chr4:15544400-15562400	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr4:15544600-15563600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:15544800-15553800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:15544800-15554600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:15544800-15571600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:15544800-15576200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr4:15545000-15559400	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr4:15545000-15575600	Weak transcription	Fetal Heart	heart
48	chr4:15545400-15556600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:15545800-15554200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:15546000-15554600	Weak transcription	Ovary	ovary

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