Variant report

Variant	rs950504
Chromosome Location	chr19:21783995-21783996
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21780063..21781970-chr19:21783251..21784988,3	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11085483	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1114305	0.80[CHB][hapmap]
rs11665855	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11880659	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11881567	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11883394	0.81[ASN][1000 genomes]
rs12459722	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12462147	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1401926	0.81[JPT][hapmap]
rs2176802	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2562402	0.80[CHB][hapmap]
rs2562456	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2650793	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2650805	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2914626	0.80[CHB][hapmap]
rs2968046	0.80[CHB][hapmap]
rs2968082	0.80[CHB][hapmap]
rs4809145	0.87[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs57879343	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58463686	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58952031	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60200684	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60206762	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60223275	0.83[ASN][1000 genomes]
rs61056366	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62108369	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62108374	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62110214	0.81[ASN][1000 genomes]
rs62110246	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6511253	0.87[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv833782	chr19:21663537-21845722	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1056332	chr19:21746555-21807647	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv911422	chr19:21752009-21973929	ZNF genes & repeats Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases
7	nsv960938	chr19:21766627-21785276	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3441368	chr19:21781459-22182822	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	esv3339694	chr19:21781479-22182792	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1063115	chr19:21782104-22528039	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription 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	38 gene(s)	inside rSNPs	diseases
11	nsv911423	chr19:21783995-21858994	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs950504	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs950504	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs950504	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs950504	RP11-678G14.3	cis	Skin Sun Exposed Lower leg	GTEx
rs950504	RP11-678G14.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21770000-21786600	Weak transcription	Primary T cells from cord blood	blood
2	chr19:21770200-21786600	Weak transcription	Right Ventricle	heart
3	chr19:21771000-21786200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr19:21771200-21786200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:21771200-21786200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr19:21771400-21785000	Weak transcription	Fetal Intestine Small	intestine
7	chr19:21778200-21785800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr19:21780600-21784400	Weak transcription	Pancreas	Pancrea
9	chr19:21781400-21785400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:21781800-21784800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:21782000-21784200	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr19:21782000-21784800	Enhancers	Dnd41	blood
13	chr19:21782000-21785000	Enhancers	K562	blood
14	chr19:21782000-21786200	Enhancers	Primary hematopoietic stem cells	blood
15	chr19:21782400-21784400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:21782600-21784000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr19:21782600-21784200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr19:21782600-21786200	Weak transcription	Spleen	Spleen
19	chr19:21782800-21784600	Weak transcription	Fetal Intestine Large	intestine
20	chr19:21783400-21784000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr19:21783400-21784000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:21783400-21784200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr19:21783600-21784000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:21783600-21784200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr19:21783600-21786200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:21783600-21787000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr19:21783800-21786000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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