Variant report

Variant	rs576861
Chromosome Location	chr1:225744337-225744338
allele	C/T
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	SETDB1	chr1:225744204-225744929	U2OS	brain:	n/a	n/a
2	GATA3	chr1:225744194-225744364	SH-SY5Y	brain:	n/a	n/a
3	POLR2A	chr1:225744277-225744873	H1-hESC	embryonic stem cell:	n/a	n/a
4	KAP1	chr1:225744175-225744717	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENAH	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10753406	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10799311	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10799314	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10799316	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap]
rs10799317	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10799318	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10799319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10915828	0.93[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.89[YRI][hapmap]
rs10915830	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10915833	0.94[EUR][1000 genomes]
rs10915834	0.92[EUR][1000 genomes]
rs10915839	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10915847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11584675	0.94[EUR][1000 genomes]
rs12028305	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1222440	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs2639703	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2639712	0.82[LWK][hapmap];0.81[TSI][hapmap]
rs2639716	0.84[EUR][1000 genomes]
rs2657564	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2657569	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs2840958	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2840967	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs2840968	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs3820226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856156	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653643	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs476540	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs487591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs498350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs510293	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs511649	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs516249	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs551996	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs554744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs554992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs561656	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426076	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6668770	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6697783	0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs6702555	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs712062	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7515907	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7524766	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7540181	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7541598	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7555139	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7555553	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs812523	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs947034	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9804142	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS 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	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs576861	ENAH	cis	normal skin	skin_eQTL
rs576861	RP11-496N12.9	cis	Thyroid	GTEx
rs576861	PYCR2	cis	cerebellum	SCAN
rs576861	LBR	cis	Artery Tibial	GTEx
rs576861	MIXL1	cis	cerebellum	SCAN
rs576861	DUSP10	cis	parietal	SCAN
rs576861	C1orf58	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225701400-225744400	Weak transcription	HUVEC	blood vessel
2	chr1:225701400-225747000	Weak transcription	Hela-S3	cervix
3	chr1:225705600-225747400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:225707200-225755000	Weak transcription	Gastric	stomach
5	chr1:225717600-225744400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:225717800-225744400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:225717800-225745000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:225717800-225747400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:225717800-225747400	Weak transcription	Fetal Stomach	stomach
10	chr1:225717800-225758200	Weak transcription	HepG2	liver
11	chr1:225718400-225756400	Weak transcription	NHLF	lung
12	chr1:225722800-225747600	Weak transcription	Fetal Intestine Small	intestine
13	chr1:225727400-225744400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:225727400-225747600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:225727400-225747600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:225727600-225753600	Weak transcription	NHEK	skin
17	chr1:225728000-225753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:225730000-225744400	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:225730200-225747600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:225730200-225753400	Weak transcription	NHDF-Ad	bronchial
21	chr1:225730200-225753600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:225730600-225747600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:225730600-225765800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:225730600-225776200	Weak transcription	Pancreas	Pancrea
25	chr1:225732000-225744400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:225732000-225744600	Weak transcription	Fetal Intestine Large	intestine
27	chr1:225732400-225763000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:225733000-225744400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:225734000-225744400	Weak transcription	Brain Angular Gyrus	brain
30	chr1:225734400-225744400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:225734600-225763600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:225735200-225744400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:225735400-225746000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:225735800-225744400	Weak transcription	A549	lung
35	chr1:225736600-225744400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:225736600-225753400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:225736600-225756200	Weak transcription	HSMMtube	muscle
38	chr1:225737000-225744400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:225737800-225756400	Weak transcription	Right Ventricle	heart
40	chr1:225738000-225744400	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:225738000-225747200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:225738000-225753600	Weak transcription	Aorta	Aorta
43	chr1:225738000-225753600	Weak transcription	Ovary	ovary
44	chr1:225738200-225744600	Weak transcription	Psoas Muscle	Psoas
45	chr1:225738200-225753400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:225738400-225745800	Weak transcription	Fetal Heart	heart
47	chr1:225738600-225758000	Weak transcription	Brain Germinal Matrix	brain
48	chr1:225738800-225744600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:225739800-225753200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:225739800-225754000	Weak transcription	Colon Smooth Muscle	Colon

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