Variant report

Variant	rs241941
Chromosome Location	chr19:38308016-38308017
allele	C/G
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	MXI1	chr19:38307680-38308594	H1-hESC	embryonic stem cell:	n/a	chr19:38308217-38308226
2	TAF1	chr19:38307876-38308302	H1-hESC	embryonic stem cell:	n/a	n/a
3	CREB1	chr19:38307699-38308669	H1-hESC	embryonic stem cell:	n/a	n/a
4	USF2	chr19:38307820-38308311	H1-hESC	embryonic stem cell:	n/a	n/a
5	USF1	chr19:38307929-38308334	H1-hESC	embryonic stem cell:	n/a	n/a
6	GTF2F1	chr19:38307810-38308129	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr19:38308000-38308150	WERI-Rb-1	eye:	n/a	n/a
8	NRF1	chr19:38307738-38308118	H1-hESC	embryonic stem cell:	n/a	n/a
9	E2F6	chr19:38307666-38308756	H1-hESC	embryonic stem cell:	n/a	chr19:38308300-38308312
10	MAX	chr19:38307648-38308717	H1-hESC	embryonic stem cell:	n/a	chr19:38308218-38308227 chr19:38308213-38308232 chr19:38308218-38308227 chr19:38308218-38308227 chr19:38308217-38308227 chr19:38308217-38308228
11	E2F6	chr19:38307625-38308636	H1-hESC	embryonic stem cell:	n/a	chr19:38308300-38308312
12	MXI1	chr19:38307632-38308820	SK-N-SH	brain:	n/a	chr19:38308217-38308226
13	MAX	chr19:38307777-38308218	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIN3A	chr19:38307779-38308631	H1-hESC	embryonic stem cell:	n/a	chr19:38308327-38308336 chr19:38308217-38308226 chr19:38308285-38308298
15	ZNF143	chr19:38307759-38308254	H1-hESC	embryonic stem cell:	n/a	chr19:38308094-38308103 chr19:38307950-38307968
16	POLR2A	chr19:38307837-38308564	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr19:38307953-38308768	H1-neurons	neurons:	n/a	n/a
18	BACH1	chr19:38307843-38308547	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr19:38307780-38308675	H1-neurons	neurons:	n/a	n/a
20	USF1	chr19:38307889-38308299	H1-hESC	embryonic stem cell:	n/a	n/a
21	USF1	chr19:38308010-38308286	ECC-1	luminal epithelium:	n/a	n/a
22	MAX	chr19:38307646-38308699	H1-hESC	embryonic stem cell:	n/a	chr19:38308218-38308227 chr19:38308213-38308232 chr19:38308218-38308227 chr19:38308218-38308227 chr19:38308217-38308227 chr19:38308217-38308228
23	NRF1	chr19:38307692-38308193	SK-N-SH	brain:	n/a	n/a
24	REST	chr19:38307930-38308908	H1-neurons	neurons:	n/a	chr19:38308320-38308330
25	MAX	chr19:38307673-38308670	ECC-1	luminal epithelium:	n/a	chr19:38308218-38308227 chr19:38308213-38308232 chr19:38308218-38308227 chr19:38308218-38308227 chr19:38308217-38308227 chr19:38308217-38308228

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIPA1L3-3	chr19:38307999-38308366	ENSG00000267640.1

Variant related genes	Relation type
ZNF573	TF binding region
ENSG00000267640	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10422056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11083438	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11665877	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11668384	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668434	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs11668558	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs11672077	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12462485	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610891	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972712	0.92[AMR][1000 genomes]
rs12981237	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12982288	0.83[AMR][1000 genomes]
rs1643470	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs1643472	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1725490	0.82[EUR][1000 genomes]
rs17306508	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs17306795	0.91[CHB][hapmap]
rs1871197	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2160640	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs241937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241946	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241947	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs241948	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs241951	0.90[CHB][hapmap]
rs241953	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs241957	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs241959	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241960	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972456	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2972459	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs34607899	0.92[AMR][1000 genomes]
rs34782935	0.83[AMR][1000 genomes]
rs34949193	0.86[AMR][1000 genomes]
rs35015599	0.92[AMR][1000 genomes]
rs35214625	0.92[AMR][1000 genomes]
rs353405	0.81[EUR][1000 genomes]
rs353406	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs353409	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs353412	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs353413	0.84[EUR][1000 genomes]
rs35415221	0.83[AMR][1000 genomes]
rs36020184	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs36092052	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3752365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs3894129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4482404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs4802134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803536	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803566	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57308437	0.83[AMR][1000 genomes]
rs62108339	0.83[AMR][1000 genomes]
rs62108355	0.85[AMR][1000 genomes]
rs6508748	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508752	0.86[EUR][1000 genomes]
rs697433	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7250668	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254170	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7254828	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7255551	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8102871	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8103882	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105694	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110417	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8111400	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs833916	0.90[CHB][hapmap]
rs856302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs856309	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs861308	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1057428	chr19:38282158-38320814	Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1062040	chr19:38294465-38370456	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38307200-38308400	Active TSS	Brain Hippocampus Middle	brain
2	chr19:38307200-38308600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:38307200-38308800	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr19:38307200-38308800	ZNF genes & repeats	Esophagus	oesophagus
5	chr19:38307400-38308200	Active TSS	Brain Germinal Matrix	brain
6	chr19:38307400-38308200	Active TSS	Fetal Brain Female	brain
7	chr19:38307400-38308400	Active TSS	Brain Angular Gyrus	brain
8	chr19:38307400-38308400	Active TSS	Brain Cingulate Gyrus	brain
9	chr19:38307400-38308400	Active TSS	Colonic Mucosa	Colon
10	chr19:38307400-38308400	ZNF genes & repeats	Fetal Intestine Large	intestine
11	chr19:38307400-38308600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
12	chr19:38307400-38308600	Active TSS	Rectal Smooth Muscle	rectum
13	chr19:38307400-38308800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
14	chr19:38307400-38308800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr19:38307400-38308800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr19:38307400-38308800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
17	chr19:38307400-38308800	ZNF genes & repeats	Liver	Liver
18	chr19:38307400-38308800	Active TSS	Fetal Kidney	kidney
19	chr19:38307400-38308800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr19:38307400-38308800	ZNF genes & repeats	NHEK	skin
21	chr19:38307400-38309000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:38307400-38309000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:38307400-38309000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr19:38307400-38309000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr19:38307400-38309400	ZNF genes & repeats	Placenta	Placenta
26	chr19:38307600-38308200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:38307600-38308200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
28	chr19:38307600-38308200	Bivalent/Poised TSS	Psoas Muscle	Psoas
29	chr19:38307600-38308400	ZNF genes & repeats	Primary B cells from cord blood	blood
30	chr19:38307600-38308400	Active TSS	NHLF	lung
31	chr19:38307600-38308600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:38307600-38308600	Active TSS	Aorta	Aorta
33	chr19:38307600-38308600	ZNF genes & repeats	Lung	lung
34	chr19:38307600-38308600	ZNF genes & repeats	HSMM	muscle
35	chr19:38307600-38308800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:38307600-38308800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:38307600-38308800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:38307600-38308800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:38307600-38308800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
40	chr19:38307600-38308800	ZNF genes & repeats	Primary T cells from cord blood	blood
41	chr19:38307600-38308800	Active TSS	Duodenum Mucosa	Duodenum
42	chr19:38307600-38308800	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr19:38307600-38308800	Active TSS	Left Ventricle	heart
44	chr19:38307600-38308800	Active TSS	Right Atrium	heart
45	chr19:38307600-38308800	Active TSS	NHDF-Ad	bronchial
46	chr19:38307600-38308800	Active TSS	Osteobl	bone
47	chr19:38307600-38309000	Active TSS	H9 Cell Line	embryonic stem cell
48	chr19:38307600-38309000	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr19:38307600-38309000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:38307600-38309000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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