Variant report

Variant	rs241942
Chromosome Location	chr19:38307904-38307905
allele	A/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	GTF2F1	chr19:38307810-38308129	H1-hESC	embryonic stem cell:	n/a	n/a
6	NRF1	chr19:38307738-38308118	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr19:38307666-38308756	H1-hESC	embryonic stem cell:	n/a	chr19:38308300-38308312
8	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
9	E2F6	chr19:38307625-38308636	H1-hESC	embryonic stem cell:	n/a	chr19:38308300-38308312
10	MXI1	chr19:38307632-38308820	SK-N-SH	brain:	n/a	chr19:38308217-38308226
11	MAX	chr19:38307777-38308218	H1-hESC	embryonic stem cell:	n/a	n/a
12	SIN3A	chr19:38307779-38308631	H1-hESC	embryonic stem cell:	n/a	chr19:38308327-38308336 chr19:38308217-38308226 chr19:38308285-38308298
13	ZNF143	chr19:38307759-38308254	H1-hESC	embryonic stem cell:	n/a	chr19:38308094-38308103 chr19:38307950-38307968
14	POLR2A	chr19:38307837-38308564	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr19:38307840-38307990	WERI-Rb-1	eye:	n/a	n/a
16	BACH1	chr19:38307843-38308547	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr19:38307780-38308675	H1-neurons	neurons:	n/a	n/a
18	USF1	chr19:38307889-38308299	H1-hESC	embryonic stem cell:	n/a	n/a
19	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
20	NRF1	chr19:38307692-38308193	SK-N-SH	brain:	n/a	n/a
21	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-WDR87-1	chr19:38307701-38307932	NONHSAT066161
2	lnc-WDR87-1	chr19:38307701-38307910	NONHSAT066162

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

Extended variants
information (count: 77 )
Associated
traits (count: 7 )

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];0.84[AFR][1000 genomes];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];0.84[AFR][1000 genomes];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	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668434	0.82[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11668558	1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs11672077	0.82[ASW][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12462485	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610891	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972712	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12981237	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12982288	0.83[AMR][1000 genomes]
rs1643470	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs1643472	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1725490	0.82[EUR][1000 genomes]
rs17306508	0.82[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17306795	0.90[CHB][hapmap]
rs1871197	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2160640	0.82[ASW][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap]
rs241937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241940	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241941	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	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241944	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241946	1.00[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[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs241951	0.90[CHB][hapmap];0.92[CHD][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	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2972459	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes]
rs34607899	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs34782935	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34949193	0.86[AMR][1000 genomes]
rs35015599	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs35214625	0.83[AFR][1000 genomes];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[AFR][1000 genomes];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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4482404	0.82[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4802134	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803536	0.84[AFR][1000 genomes];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[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs62108355	0.85[AMR][1000 genomes]
rs6508748	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508752	0.86[EUR][1000 genomes]
rs697433	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7250668	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254170	0.82[ASW][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.83[AFR][1000 genomes]
rs7254828	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][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	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105694	0.84[AFR][1000 genomes];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	1.00[CHB][hapmap]
rs856302	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs856309	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs861308	1.00[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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs241942	CEACAM16	cis	parietal	SCAN
rs241942	ARHGEF1	cis	cerebellum	SCAN
rs241942	GSK3A	cis	parietal	SCAN
rs241942	TMEM145	cis	parietal	SCAN
rs241942	PPP5C	cis	parietal	SCAN
rs241942	ITPKC	cis	cerebellum	SCAN
rs241942	CD3EAP	cis	cerebellum	SCAN

Chromatin state (count:105 , 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	chr19:38307400-38308000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
6	chr19:38307400-38308000	Flanking Active TSS	Fetal Brain Male	brain
7	chr19:38307400-38308200	Active TSS	Brain Germinal Matrix	brain
8	chr19:38307400-38308200	Active TSS	Fetal Brain Female	brain
9	chr19:38307400-38308400	Active TSS	Brain Angular Gyrus	brain
10	chr19:38307400-38308400	Active TSS	Brain Cingulate Gyrus	brain
11	chr19:38307400-38308400	Active TSS	Colonic Mucosa	Colon
12	chr19:38307400-38308400	ZNF genes & repeats	Fetal Intestine Large	intestine
13	chr19:38307400-38308600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
14	chr19:38307400-38308600	Active TSS	Rectal Smooth Muscle	rectum
15	chr19:38307400-38308800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
16	chr19:38307400-38308800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:38307400-38308800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
18	chr19:38307400-38308800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
19	chr19:38307400-38308800	ZNF genes & repeats	Liver	Liver
20	chr19:38307400-38308800	Active TSS	Fetal Kidney	kidney
21	chr19:38307400-38308800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr19:38307400-38308800	ZNF genes & repeats	NHEK	skin
23	chr19:38307400-38309000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:38307400-38309000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:38307400-38309000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:38307400-38309000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
27	chr19:38307400-38309400	ZNF genes & repeats	Placenta	Placenta
28	chr19:38307600-38308000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
29	chr19:38307600-38308000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:38307600-38308000	Flanking Active TSS	Fetal Muscle Trunk	muscle
31	chr19:38307600-38308000	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr19:38307600-38308000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
33	chr19:38307600-38308000	Active TSS	Stomach Smooth Muscle	stomach
34	chr19:38307600-38308000	Active TSS	NH-A	brain
35	chr19:38307600-38308200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:38307600-38308200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
37	chr19:38307600-38308200	Bivalent/Poised TSS	Psoas Muscle	Psoas
38	chr19:38307600-38308400	ZNF genes & repeats	Primary B cells from cord blood	blood
39	chr19:38307600-38308400	Active TSS	NHLF	lung
40	chr19:38307600-38308600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:38307600-38308600	Active TSS	Aorta	Aorta
42	chr19:38307600-38308600	ZNF genes & repeats	Lung	lung
43	chr19:38307600-38308600	ZNF genes & repeats	HSMM	muscle
44	chr19:38307600-38308800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:38307600-38308800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:38307600-38308800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:38307600-38308800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:38307600-38308800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
49	chr19:38307600-38308800	ZNF genes & repeats	Primary T cells from cord blood	blood
50	chr19:38307600-38308800	Active TSS	Duodenum Mucosa	Duodenum

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