Variant report

Variant	rs241950
Chromosome Location	chr19:38269133-38269134
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIX5	chr19:38269120-38270827	A549	lung:	n/a	n/a
2	MXI1	chr19:38269054-38271214	SK-N-SH	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38085182..38087082-chr19:38268049..38270346,2	K562	blood:
2	chr19:38261551..38263090-chr19:38267286..38270188,2	K562	blood:
3	chr19:37956743..37958791-chr19:38268721..38270290,2	K562	blood:
4	chr19:38259097..38263090-chr19:38267286..38270188,4	K562	blood:
5	chr19:37995858..37997705-chr19:38268751..38270937,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF573	TF binding region
ENSG00000267422	TF binding region
ENSG00000266916	Chromatin interaction
ENSG00000196437	Chromatin interaction
ENSG00000171827	Chromatin interaction
ENSG00000180479	Chromatin interaction
ENSG00000171817	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10048511	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10401968	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10402530	0.83[EUR][1000 genomes]
rs10409402	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10409487	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10420746	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10420891	0.83[EUR][1000 genomes]
rs11673023	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11878269	0.84[EUR][1000 genomes]
rs11879180	0.83[EUR][1000 genomes]
rs1291	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12974225	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12975057	0.83[EUR][1000 genomes]
rs12979640	0.81[ASN][1000 genomes]
rs171376	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1974714	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2075281	0.84[EUR][1000 genomes]
rs2075284	0.83[ASN][1000 genomes]
rs2287229	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs241932	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs241933	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2909085	0.81[ASN][1000 genomes]
rs2909088	0.81[ASN][1000 genomes]
rs2909093	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2909098	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2909100	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2909102	0.81[ASN][1000 genomes]
rs2909105	0.81[ASN][1000 genomes]
rs2909109	0.81[ASN][1000 genomes]
rs2972434	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972437	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972438	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972439	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972445	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3095724	0.84[ASN][1000 genomes]
rs3095726	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3112434	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3848626	0.83[EUR][1000 genomes]
rs4802135	0.81[EUR][1000 genomes]
rs4803509	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803524	0.83[EUR][1000 genomes]
rs6508742	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257125	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8101752	0.83[EUR][1000 genomes]
rs8101858	0.80[EUR][1000 genomes]
rs8102579	0.83[EUR][1000 genomes]
rs8103633	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8104076	0.84[EUR][1000 genomes]
rs8112706	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8182498	0.83[EUR][1000 genomes]
rs856300	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs856304	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304569	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs958305	0.81[EUR][1000 genomes]
rs968073	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS 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 target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs241950	ZNF571	cis	multi-tissue	Pritchard

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38231800-38269200	Weak transcription	Fetal Brain Male	brain
2	chr19:38236400-38269400	Weak transcription	Aorta	Aorta
3	chr19:38238800-38269400	Weak transcription	Small Intestine	intestine
4	chr19:38239000-38269400	Weak transcription	Colonic Mucosa	Colon
5	chr19:38247800-38269200	Weak transcription	Hela-S3	cervix
6	chr19:38248800-38269400	Weak transcription	NH-A	brain
7	chr19:38249800-38269400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr19:38251800-38269400	Weak transcription	Gastric	stomach
9	chr19:38251800-38269400	Weak transcription	HUVEC	blood vessel
10	chr19:38252200-38269400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:38254600-38269400	Weak transcription	Right Ventricle	heart
12	chr19:38254800-38269200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:38256800-38269400	Weak transcription	NHLF	lung
14	chr19:38258800-38269200	Weak transcription	HSMMtube	muscle
15	chr19:38259200-38269200	Weak transcription	Brain Angular Gyrus	brain
16	chr19:38259200-38269200	Weak transcription	Fetal Kidney	kidney
17	chr19:38259200-38269200	Weak transcription	HSMM	muscle
18	chr19:38259200-38269400	Weak transcription	Psoas Muscle	Psoas
19	chr19:38259400-38269200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:38260200-38269200	Weak transcription	Fetal Thymus	thymus
21	chr19:38260800-38269200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr19:38260800-38269200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:38260800-38269400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:38260800-38269400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr19:38261000-38269200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr19:38261000-38269200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr19:38261000-38269200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr19:38261000-38269200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr19:38261200-38269200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr19:38261200-38269200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:38261200-38269200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr19:38261200-38269200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:38261200-38269200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr19:38261200-38269200	Weak transcription	HepG2	liver
35	chr19:38261200-38269200	Weak transcription	Osteobl	bone
36	chr19:38261200-38269400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:38261200-38269400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr19:38261200-38269400	Weak transcription	Esophagus	oesophagus
39	chr19:38261200-38269400	Weak transcription	Fetal Muscle Leg	muscle
40	chr19:38261200-38269400	Weak transcription	Placenta	Placenta
41	chr19:38261200-38269400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr19:38261400-38269200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:38261400-38269200	Weak transcription	Brain Germinal Matrix	brain
44	chr19:38261400-38269200	Weak transcription	Fetal Lung	lung
45	chr19:38262200-38269200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr19:38262400-38269200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:38262400-38269200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:38262400-38269200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr19:38262600-38269200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr19:38262600-38269200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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