Variant report

Variant	rs7246569
Chromosome Location	chr19:20013987-20013988
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:20012007..20015625-chr19:20016618..20018648,3	K562	blood:
2	chr19:20012861..20014472-chr19:20018867..20021328,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1019279	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10403255	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10407726	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10408752	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10412710	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10414919	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10415179	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10421280	0.86[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap]
rs10426937	0.88[EUR][1000 genomes]
rs1048421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12151060	0.82[CEU][hapmap]
rs13344370	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1469700	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs1469701	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs17617402	0.84[ASW][hapmap]
rs2060239	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2160156	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2335365	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2335366	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2335368	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2335887	0.84[ASW][hapmap]
rs28590063	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs386976	0.84[ASW][hapmap]
rs3943792	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808221	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs4809006	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4809015	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4809016	0.86[ASN][1000 genomes]
rs55816500	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60765256	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511059	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66970424	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252079	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7253407	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7254355	0.88[EUR][1000 genomes]
rs7256224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7258260	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73532705	0.82[EUR][1000 genomes]
rs8105329	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8105482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8108528	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109743	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8113576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8113694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv911316	chr19:19890450-20021046	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv961192	chr19:19906394-20083740	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
8	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
9	esv3413756	chr19:19936066-20072059	ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	esv3380276	chr19:19936583-20073601	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv3429980	chr19:19943721-20102072	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1061846	chr19:19946927-20595412	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
13	esv3390957	chr19:19965887-20819154	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
14	nsv869122	chr19:19969851-20595412	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
15	nsv1057569	chr19:19973268-20193556	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	nsv1059158	chr19:19973489-20576161	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
17	esv3407363	chr19:20000919-20059307	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	esv1845482	chr19:20006144-20014389	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7246569	ZNF493	cis	parietal	SCAN
rs7246569	ZNF682	cis	Muscle Skeletal	GTEx
rs7246569	C19orf44	cis	cerebellum	SCAN
rs7246569	ZNF253	cis	Nerve Tibial	GTEx
rs7246569	ATP13A1	cis	parietal	SCAN
rs7246569	SUGP2	cis	parietal	SCAN
rs7246569	HOMER3	cis	cerebellum	SCAN
rs7246569	ZNF506	cis	cerebellum	SCAN
rs7246569	GTPBP3	cis	parietal	SCAN
rs7246569	ZNF93	cis	Thyroid	GTEx
rs7246569	ZNF93	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:20011000-20014000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr19:20011000-20014000	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr19:20011000-20014400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr19:20012600-20030000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:20012800-20014000	Enhancers	Primary T cells fromperipheralblood	blood
6	chr19:20012800-20017200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
7	chr19:20012800-20034200	Weak transcription	Pancreas	Pancrea
8	chr19:20012800-20034200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr19:20012800-20034600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr19:20012800-20043400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr19:20013000-20014000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:20013000-20014000	Weak transcription	Fetal Intestine Small	intestine
13	chr19:20013000-20014000	Weak transcription	Thymus	Thymus
14	chr19:20013000-20014400	Transcr. at gene 5' and 3'	Dnd41	blood
15	chr19:20013000-20014600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:20013000-20015400	Weak transcription	Right Ventricle	heart
17	chr19:20013000-20016000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:20013000-20019000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr19:20013000-20019800	Weak transcription	HSMM	muscle
20	chr19:20013000-20022600	Weak transcription	Aorta	Aorta
21	chr19:20013000-20024200	Weak transcription	Ovary	ovary
22	chr19:20013000-20034000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:20013000-20034600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr19:20013000-20034600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr19:20013000-20035200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr19:20013000-20039600	Weak transcription	Colon Smooth Muscle	Colon
27	chr19:20013200-20014000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:20013200-20014000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:20013200-20014200	Weak transcription	Fetal Stomach	stomach
30	chr19:20013200-20014600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr19:20013200-20015200	Weak transcription	NH-A	brain
32	chr19:20013200-20015600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr19:20013200-20016200	ZNF genes & repeats	Primary B cells from cord blood	blood
34	chr19:20013200-20016600	Weak transcription	NHDF-Ad	bronchial
35	chr19:20013200-20016800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr19:20013200-20017200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr19:20013200-20017400	Weak transcription	Fetal Lung	lung
38	chr19:20013200-20019600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr19:20013200-20021800	Weak transcription	Fetal Heart	heart
40	chr19:20013200-20026000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:20013200-20026200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr19:20013200-20027400	Weak transcription	HSMMtube	muscle
43	chr19:20013200-20027600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr19:20013200-20028600	Weak transcription	Adipose Nuclei	Adipose
45	chr19:20013200-20028800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
46	chr19:20013200-20034600	Weak transcription	Primary T cells from cord blood	blood
47	chr19:20013200-20043600	Weak transcription	Fetal Brain Male	brain
48	chr19:20013400-20014000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr19:20013400-20014000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:20013400-20014000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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