Variant report

Variant	rs4729616
Chromosome Location	chr7:100462565-100462566
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1054391	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11973000	0.91[EUR][1000 genomes]
rs12666785	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12669120	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12672665	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12705094	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12705097	0.86[EUR][1000 genomes]
rs13225631	0.84[EUR][1000 genomes]
rs13226043	0.96[ASN][1000 genomes]
rs13232524	0.89[EUR][1000 genomes]
rs13240020	0.84[EUR][1000 genomes]
rs13241786	0.85[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs15624	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1799806	0.86[EUR][1000 genomes]
rs2405973	0.90[EUR][1000 genomes]
rs2405974	0.89[EUR][1000 genomes]
rs2405975	0.92[EUR][1000 genomes]
rs2571598	0.94[EUR][1000 genomes]
rs28852509	0.83[EUR][1000 genomes]
rs2894713	0.92[EUR][1000 genomes]
rs3087504	0.92[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs314329	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs314332	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs314368	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs314369	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs314371	0.98[ASN][1000 genomes]
rs314372	0.96[ASN][1000 genomes]
rs314374	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs314375	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs314376	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs314377	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs314378	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34005963	0.92[EUR][1000 genomes]
rs3757869	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3757870	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3757871	0.91[EUR][1000 genomes]
rs3843541	0.84[EUR][1000 genomes]
rs3843542	0.86[EUR][1000 genomes]
rs3847063	0.92[CEU][hapmap]
rs3847064	0.92[EUR][1000 genomes]
rs3847068	0.91[EUR][1000 genomes]
rs3931823	0.92[EUR][1000 genomes]
rs4727469	0.92[CEU][hapmap]
rs4729615	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4729617	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4729618	0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs4729619	0.92[EUR][1000 genomes]
rs4729620	0.92[CEU][hapmap]
rs6465776	0.83[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6942607	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6954151	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6976053	0.89[CEU][hapmap]
rs7783457	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7783543	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7798613	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7801015	0.96[ASN][1000 genomes]
rs7803865	0.92[CEU][hapmap]
rs9718841	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv464647	chr7:100374087-100497131	Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv607965	chr7:100374087-100497131	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv1032673	chr7:100382250-100606794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
9	nsv888797	chr7:100386900-100482026	Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
10	nsv888798	chr7:100406144-100472826	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	nsv888799	chr7:100406144-100497131	Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
12	nsv888801	chr7:100416250-100497131	Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv464648	chr7:100422156-100518458	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
14	nsv607966	chr7:100422156-100518458	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
15	nsv831073	chr7:100425659-100544888	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4729616	FAM185A	cis	cerebellum	SCAN
rs4729616	TRRAP	cis	cerebellum	SCAN
rs4729616	SHFM1	cis	cerebellum	SCAN
rs4729616	ZNF3	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100451000-100463200	Weak transcription	HSMMtube	muscle
2	chr7:100451000-100464200	Weak transcription	Left Ventricle	heart
3	chr7:100451000-100464200	Weak transcription	Small Intestine	intestine
4	chr7:100451000-100464400	Weak transcription	Fetal Kidney	kidney
5	chr7:100451200-100463200	Weak transcription	A549	lung
6	chr7:100451200-100463200	Weak transcription	Hela-S3	cervix
7	chr7:100451200-100463200	Weak transcription	NHDF-Ad	bronchial
8	chr7:100451200-100463800	Weak transcription	Right Atrium	heart
9	chr7:100451200-100464200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:100451400-100464200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr7:100451800-100462800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:100451800-100464200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr7:100452000-100463400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr7:100452000-100463600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr7:100452200-100463000	Strong transcription	Lung	lung
16	chr7:100452200-100463400	Strong transcription	Fetal Stomach	stomach
17	chr7:100452200-100463600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:100452400-100463200	Weak transcription	Fetal Brain Male	brain
19	chr7:100452400-100464000	Weak transcription	GM12878-XiMat	blood
20	chr7:100452800-100463400	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr7:100453000-100463200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr7:100453200-100463600	Strong transcription	Thymus	Thymus
23	chr7:100453200-100464200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr7:100453400-100463000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr7:100453400-100463000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr7:100454400-100463400	Strong transcription	Primary T cells from cord blood	blood
27	chr7:100454800-100464200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr7:100455000-100463400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr7:100456200-100463200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr7:100456200-100463400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
31	chr7:100456400-100462600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr7:100456400-100463400	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr7:100456400-100464200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr7:100456600-100463000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr7:100456600-100463200	Strong transcription	Primary B cells from cord blood	blood
36	chr7:100458200-100463400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr7:100458600-100463000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr7:100458600-100463000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr7:100458800-100462600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:100459000-100463200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr7:100459000-100464400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr7:100459200-100462800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr7:100459200-100464000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:100459200-100464200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr7:100459200-100464200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr7:100459200-100464400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr7:100459400-100463400	Weak transcription	Pancreas	Pancrea
48	chr7:100459400-100464200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr7:100459600-100463200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:100459600-100463200	Weak transcription	Right Ventricle	heart

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