Variant report

Variant	rs66509430
Chromosome Location	chr7:64147935-64147936
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:64147661-64147986	Raji	blood:	n/a	n/a
2	POLR2A	chr7:64147569-64148088	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF138-3	chr7:64144713-64148208	NR_104148
2	lnc-ZNF138-3	chr7:64144713-64148208	NR_104149

Variant related genes	Relation type
ZNF107	TF binding region
ENSG00000271550	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10085367	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10247618	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10248287	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10253381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10273013	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11766737	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11769008	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11972903	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11974709	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11980700	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17779736	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28537641	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2862794	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28879694	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34676383	0.82[AFR][1000 genomes]
rs3750027	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3750029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56955205	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58101050	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6460176	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6460178	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6944545	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6944849	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6946200	0.86[EUR][1000 genomes]
rs6949440	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6955970	0.87[EUR][1000 genomes]
rs6963252	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6966466	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6969837	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6970764	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6973333	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6973346	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6975253	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6975404	0.84[EUR][1000 genomes]
rs73136779	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73136786	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73136802	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73138703	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73138715	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7782515	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7802372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7804972	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9791622	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

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	nsv427787	chr7:63741770-64419520	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv2764000	chr7:63766980-64275251	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
4	esv2755057	chr7:63819849-64345822	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
5	nsv1031703	chr7:63839601-64225952	Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
6	nsv464518	chr7:63881238-64506904	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv607312	chr7:63881238-64506904	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv888271	chr7:63961212-64295884	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv888273	chr7:63990100-64291622	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
10	nsv888274	chr7:63990100-64331123	Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
11	nsv888275	chr7:63990100-64468590	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv888276	chr7:63990100-64511564	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
13	nsv1021893	chr7:63995601-64155027	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
14	nsv538892	chr7:63995601-64155027	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
15	esv16290	chr7:64058602-64162829	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
16	nsv888279	chr7:64094285-64331123	Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
17	nsv970856	chr7:64126256-64155821	Strong transcription Active TSS ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs66509430	ZNF138	cis	Skin Sun Exposed Lower leg	GTEx
rs66509430	ZNF107	cis	Esophagus Mucosa	GTEx
rs66509430	ZNF107	cis	Skin Sun Exposed Lower leg	GTEx
rs66509430	RP11-561N12.7	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64127400-64153600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:64128200-64167600	Weak transcription	Hela-S3	cervix
3	chr7:64128200-64168000	Weak transcription	Brain Angular Gyrus	brain
4	chr7:64128800-64168000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:64138400-64152600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr7:64138600-64153000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr7:64138600-64162200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:64138600-64168400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:64138800-64153000	ZNF genes & repeats	GM12878-XiMat	blood
10	chr7:64139000-64149000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:64139400-64148000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr7:64139400-64148000	ZNF genes & repeats	Fetal Intestine Small	intestine
13	chr7:64139400-64148000	ZNF genes & repeats	Thymus	Thymus
14	chr7:64139400-64148600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:64139400-64148600	ZNF genes & repeats	Brain Germinal Matrix	brain
16	chr7:64139400-64153000	ZNF genes & repeats	Fetal Brain Female	brain
17	chr7:64139400-64155000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
18	chr7:64139600-64148000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:64139600-64148000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr7:64139600-64149000	ZNF genes & repeats	Fetal Thymus	thymus
21	chr7:64139800-64148000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
22	chr7:64140800-64148000	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr7:64140800-64148600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr7:64141000-64148000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:64141000-64159800	Weak transcription	Stomach Mucosa	stomach
26	chr7:64141200-64148000	ZNF genes & repeats	Spleen	Spleen
27	chr7:64141400-64148000	Strong transcription	Pancreas	Pancrea
28	chr7:64141400-64149600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:64142800-64149000	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr7:64143200-64148000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr7:64143200-64148200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:64143200-64148600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr7:64143600-64148600	Strong transcription	Left Ventricle	heart
34	chr7:64143800-64167000	Weak transcription	Fetal Heart	heart
35	chr7:64144800-64148200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
36	chr7:64145200-64148000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr7:64145400-64159800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr7:64145400-64166800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr7:64145600-64163000	Weak transcription	Right Ventricle	heart
40	chr7:64145800-64150000	Weak transcription	Brain Hippocampus Middle	brain
41	chr7:64145800-64154000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr7:64145800-64154400	Weak transcription	NHDF-Ad	bronchial
43	chr7:64145800-64156400	Weak transcription	Ovary	ovary
44	chr7:64145800-64156600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr7:64146000-64148800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
46	chr7:64146000-64154400	Weak transcription	NHLF	lung
47	chr7:64146000-64167000	Weak transcription	Brain Substantia Nigra	brain
48	chr7:64146200-64148000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr7:64146200-64148200	ZNF genes & repeats	A549	lung
50	chr7:64146200-64149800	Weak transcription	Rectal Smooth Muscle	rectum

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