Variant report

Variant	rs60041535
Chromosome Location	chr19:19922203-19922204
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10407920	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10412409	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10419635	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10854013	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11878280	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12461018	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12973032	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12975121	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304171	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2335360	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs23654	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248938	0.80[EUR][1000 genomes]
rs248939	0.83[EUR][1000 genomes]
rs248940	0.83[EUR][1000 genomes]
rs248941	0.82[EUR][1000 genomes]
rs248955	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2878398	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34277739	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35018071	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35280091	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4990741	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7246983	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252985	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8104136	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8108416	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs919785	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv458375	chr19:19863014-19949209	Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv578798	chr19:19863014-19949209	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv911313	chr19:19866371-19936078	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription 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	15 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	nsv578799	chr19:19901136-19967970	ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60041535	ZNF506	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19888400-19927800	Weak transcription	Psoas Muscle	Psoas
2	chr19:19888600-19931800	Weak transcription	Fetal Heart	heart
3	chr19:19895000-19931200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:19902600-19922400	Weak transcription	Right Ventricle	heart
5	chr19:19902600-19931600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:19905000-19930000	Weak transcription	Colon Smooth Muscle	Colon
7	chr19:19906400-19923200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:19907000-19923200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr19:19907000-19931400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:19907000-19931600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr19:19907600-19929600	Weak transcription	Small Intestine	intestine
12	chr19:19907800-19931600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:19908000-19931600	Weak transcription	Stomach Mucosa	stomach
14	chr19:19909200-19931600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:19914200-19924600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr19:19914200-19926200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr19:19914400-19922400	Weak transcription	Left Ventricle	heart
18	chr19:19914400-19922400	Weak transcription	Ovary	ovary
19	chr19:19914400-19922400	Weak transcription	Pancreas	Pancrea
20	chr19:19914400-19922400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr19:19914400-19922600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr19:19914400-19924600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:19914400-19925400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:19914400-19926000	Weak transcription	Brain Substantia Nigra	brain
25	chr19:19914400-19926000	Weak transcription	Spleen	Spleen
26	chr19:19914400-19927600	Weak transcription	Gastric	stomach
27	chr19:19914400-19927800	Weak transcription	Aorta	Aorta
28	chr19:19914400-19929600	Weak transcription	HSMMtube	muscle
29	chr19:19914400-19931400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:19914400-19931600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:19914600-19923200	Weak transcription	Colonic Mucosa	Colon
32	chr19:19914600-19925600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:19914800-19924600	Weak transcription	Fetal Brain Female	brain
34	chr19:19914800-19925400	Weak transcription	NH-A	brain
35	chr19:19915200-19929600	Weak transcription	NHLF	lung
36	chr19:19915800-19923200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:19915800-19926800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
38	chr19:19915800-19930400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:19916200-19931200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
40	chr19:19916800-19931600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr19:19917000-19923000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:19917000-19923000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr19:19917000-19923200	Weak transcription	NHDF-Ad	bronchial
44	chr19:19917000-19924400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr19:19917000-19924800	Weak transcription	HSMM	muscle
46	chr19:19917000-19929400	Weak transcription	Fetal Brain Male	brain
47	chr19:19917000-19931400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr19:19917000-19931600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:19917200-19924400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:19917400-19922400	Weak transcription	Fetal Muscle Leg	muscle

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