Variant report

Variant	rs1709474
Chromosome Location	chr7:64561863-64561864
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10234467	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10949955	0.88[CEU][hapmap]
rs12056103	0.95[YRI][hapmap]
rs13223327	0.85[CEU][hapmap]
rs1540833	0.92[CEU][hapmap]
rs1709473	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1709475	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17710097	0.89[CEU][hapmap]
rs17782771	0.89[CEU][hapmap]
rs1818916	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap]
rs2091224	0.92[CEU][hapmap]
rs2103148	1.00[CEU][hapmap]
rs2419256	1.00[CEU][hapmap]
rs2419281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2671945	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2671946	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28877001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2900628	0.89[CEU][hapmap]
rs2900858	0.89[CEU][hapmap]
rs34739196	0.89[CEU][hapmap]
rs35513558	0.89[CEU][hapmap]
rs3807068	0.92[CEU][hapmap]
rs3807069	0.85[CEU][hapmap]
rs3823471	0.93[CEU][hapmap]
rs3899200	0.89[CEU][hapmap]
rs4718180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs4718188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4718190	0.96[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4718207	0.89[CEU][hapmap]
rs4718211	0.93[CEU][hapmap]
rs495336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs517258	0.92[CEU][hapmap]
rs549970	0.85[CEU][hapmap]
rs593619	0.85[CEU][hapmap]
rs594456	0.89[CEU][hapmap]
rs608809	0.93[CEU][hapmap]
rs6460216	0.89[CEU][hapmap]
rs6460230	0.88[CEU][hapmap]
rs6460232	0.92[CEU][hapmap]
rs657560	0.84[CEU][hapmap]
rs658360	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs658606	0.84[CEU][hapmap]
rs666389	0.93[CEU][hapmap]
rs673957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7780100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7792874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs7796077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7799516	0.89[CEU][hapmap]
rs7806567	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:55 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422405	chr7:63709739-64632341	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1022042	chr7:64226499-64566945	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv3506582	chr7:64323055-64563984	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3506583	chr7:64323055-64563984	Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	esv2752165	chr7:64345822-65208605	Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv888284	chr7:64406439-64562139	ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv1033517	chr7:64443052-64942418	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv538893	chr7:64443052-64942418	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv1034625	chr7:64456197-64850413	Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
10	nsv1019089	chr7:64456197-64874187	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
11	nsv1023699	chr7:64456197-64942418	Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv517778	chr7:64462326-65326821	ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
13	nsv429767	chr7:64473713-65415647	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
14	nsv917231	chr7:64478253-65300317	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
15	esv34341	chr7:64478386-65012082	Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
16	esv2752166	chr7:64478386-65208605	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
17	nsv1029796	chr7:64494934-65302696	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
18	nsv916005	chr7:64499811-65012082	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
19	nsv533081	chr7:64499945-65208605	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
20	esv3339156	chr7:64510176-65349050	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
21	nsv888285	chr7:64511564-64662075	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
22	nsv888286	chr7:64529883-64800432	Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	esv18831	chr7:64534085-64581674	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
24	nsv888287	chr7:64537992-64990806	Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
25	nsv966822	chr7:64541569-64585100	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
26	esv1823506	chr7:64546212-64566133	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
27	esv1806768	chr7:64547701-64562185	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers	lncRNA	n/a	inside rSNPs	diseases
28	esv1824216	chr7:64547701-64566333	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS	lncRNA	n/a	inside rSNPs	diseases
29	esv1810799	chr7:64547901-64561985	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers	lncRNA	n/a	inside rSNPs	diseases
30	esv1809839	chr7:64547901-64566133	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS	lncRNA	n/a	inside rSNPs	diseases
31	esv1848366	chr7:64547901-64566133	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS	lncRNA	n/a	inside rSNPs	diseases
32	esv1806464	chr7:64548196-64582972	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers	lncRNA	n/a	inside rSNPs	diseases
33	esv1808300	chr7:64548196-64582972	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	inside rSNPs	diseases
34	esv1820759	chr7:64548196-64582972	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS	lncRNA	n/a	inside rSNPs	diseases
35	esv1848854	chr7:64548196-64582972	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS	lncRNA	n/a	inside rSNPs	diseases
36	esv1808582	chr7:64548396-64582772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS	lncRNA	n/a	inside rSNPs	diseases
37	esv1817760	chr7:64548396-64582772	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
38	esv1806713	chr7:64548788-64566333	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
39	esv11772	chr7:64550072-64568299	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers	lncRNA	n/a	inside rSNPs	diseases
40	esv2758117	chr7:64551274-65208605	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
41	esv2759534	chr7:64551274-65373851	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
42	nsv427788	chr7:64551274-65390424	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
43	nsv8120	chr7:64551526-64566984	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS	lncRNA	n/a	inside rSNPs	diseases
44	esv1844539	chr7:64552039-64582972	Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers	lncRNA	n/a	inside rSNPs	diseases
45	esv1813040	chr7:64552239-64566133	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers	lncRNA	n/a	inside rSNPs	diseases
46	esv1824070	chr7:64552239-64566133	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS	lncRNA	n/a	inside rSNPs	diseases
47	esv1843193	chr7:64552239-64566133	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
48	esv1812612	chr7:64552239-64582772	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
49	esv1824856	chr7:64552239-64582772	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS	lncRNA	n/a	inside rSNPs	diseases
50	esv1845972	chr7:64552239-64582772	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs1709474	RP11-460N20.5	cis	Esophagus Mucosa	GTEx
rs1709474	RP11-797H7.3	cis	Thyroid	GTEx
rs1709474	RP11-667F9.1	cis	Adipose Subcutaneous	GTEx
rs1709474	RP11-460N20.5	cis	Whole Blood	GTEx
rs1709474	RP11-797H7.3	cis	Whole Blood	GTEx
rs1709474	CCT6P3	cis	Esophagus Mucosa	GTEx
rs1709474	CCT6P3	cis	Nerve Tibial	GTEx
rs1709474	ZNF273	cis	Thyroid	GTEx
rs1709474	RP11-797H7.3	cis	Artery Tibial	GTEx
rs1709474	AC104057.1	cis	Adipose Subcutaneous	GTEx
rs1709474	RP11-460N20.4	cis	Adipose Subcutaneous	GTEx
rs1709474	INTS4L1	cis	Esophagus Muscularis	GTEx
rs1709474	RP11-460N20.4	cis	Esophagus Mucosa	GTEx
rs1709474	RP11-460N20.5	cis	Nerve Tibial	GTEx
rs1709474	RP11-460N20.5	cis	Adipose Subcutaneous	GTEx
rs1709474	RP11-797H7.5	cis	Adipose Subcutaneous	GTEx
rs1709474	RP11-667F9.1	cis	Nerve Tibial	GTEx
rs1709474	RP11-797H7.5	cis	Thyroid	GTEx
rs1709474	RP11-797H7.3	cis	Adipose Subcutaneous	GTEx
rs1709474	INTS4L1	cis	Nerve Tibial	GTEx
rs1709474	CCT6P3	cis	Adipose Subcutaneous	GTEx
rs1709474	RP11-460N20.5	cis	Thyroid	GTEx
rs1709474	CCT6P3	cis	Skin Sun Exposed Lower leg	GTEx
rs1709474	ZNF273	cis	lung	GTEx
rs1709474	INTS4L1	cis	Skin Sun Exposed Lower leg	GTEx
rs1709474	RP11-460N20.5	cis	lung	GTEx
rs1709474	RP11-797H7.3	cis	lung	GTEx
rs1709474	RP11-460N20.5	cis	Artery Tibial	GTEx
rs1709474	RP11-797H7.5	cis	lung	GTEx
rs1709474	INTS4L1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64542000-64562200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:64542000-64563200	Weak transcription	Left Ventricle	heart
3	chr7:64542000-64571000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:64542200-64563800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr7:64542200-64567000	Weak transcription	Right Ventricle	heart
6	chr7:64542200-64568200	Weak transcription	Adipose Nuclei	Adipose
7	chr7:64542400-64562600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr7:64542400-64562800	Weak transcription	K562	blood
9	chr7:64542400-64565400	Weak transcription	Fetal Brain Female	brain
10	chr7:64542400-64565600	Weak transcription	HSMMtube	muscle
11	chr7:64542400-64573400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr7:64549600-64564600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr7:64550400-64566800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:64553600-64567200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr7:64553800-64564800	Weak transcription	Ovary	ovary
16	chr7:64561000-64562000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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