Variant report

Variant	rs3820226
Chromosome Location	chr1:225687981-225687982
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225686982..225689320-chr1:225964805..225966549,2	MCF-7	breast:
2	chr1:225674187..225676643-chr1:225684973..225688505,3	K562	blood:

Variant related genes	Relation type
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10753406	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10799311	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10799313	0.84[ASN][1000 genomes]
rs10799314	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10799316	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.85[ASN][1000 genomes]
rs10799317	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10799318	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10799319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915828	0.93[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[YRI][hapmap]
rs10915830	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10915833	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10915834	0.93[EUR][1000 genomes]
rs10915835	0.84[ASN][1000 genomes]
rs10915837	0.85[ASN][1000 genomes]
rs10915838	0.81[ASN][1000 genomes]
rs10915839	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10915847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11584675	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12028305	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1222440	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs12729655	0.85[ASN][1000 genomes]
rs2639703	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2639712	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs2639716	0.81[EUR][1000 genomes]
rs2657564	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2657569	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs2840958	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2840967	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs2840968	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs3856156	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653643	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs476540	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs487591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs498350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs510293	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs511649	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs516249	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs551996	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs554744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs554992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs561656	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs576861	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]
rs6426076	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6426078	0.84[ASN][1000 genomes]
rs6668770	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6676201	0.85[ASN][1000 genomes]
rs6678806	0.85[ASN][1000 genomes]
rs6697783	0.94[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs6702555	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712062	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7515907	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7515963	0.85[ASN][1000 genomes]
rs7524766	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7540181	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7541598	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7555139	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7555553	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs812523	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs947034	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9804142	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv873227	chr1:225656388-225687981	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv873228	chr1:225665284-225687981	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	esv2756886	chr1:225665694-225703485	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	esv2759003	chr1:225665694-225703485	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv873230	chr1:225668524-225687981	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv4720	chr1:225673218-225718009	Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3820226	LBR	cis	Artery Tibial	GTEx
rs3820226	MIXL1	cis	cerebellum	SCAN
rs3820226	C1orf58	cis	parietal	SCAN
rs3820226	ENAH	cis	normal skin	skin_eQTL
rs3820226	DUSP10	cis	parietal	SCAN
rs3820226	RP11-496N12.9	cis	Thyroid	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225663200-225696400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:225666000-225696800	Weak transcription	Esophagus	oesophagus
3	chr1:225669800-225696800	Weak transcription	Pancreas	Pancrea
4	chr1:225670800-225688400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:225672200-225696800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:225672200-225696800	Weak transcription	Brain Germinal Matrix	brain
7	chr1:225672800-225693800	Weak transcription	Left Ventricle	heart
8	chr1:225673600-225693800	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:225674400-225696800	Weak transcription	Aorta	Aorta
10	chr1:225674800-225693800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:225676200-225696400	Weak transcription	Gastric	stomach
12	chr1:225677200-225688400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:225677200-225688400	Weak transcription	Brain Anterior Caudate	brain
14	chr1:225677200-225696000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:225677200-225696400	Weak transcription	Brain Angular Gyrus	brain
16	chr1:225677200-225696400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:225677200-225696400	Weak transcription	Brain Substantia Nigra	brain
18	chr1:225677200-225696400	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:225677200-225696600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:225677200-225696600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:225677200-225696600	Weak transcription	Psoas Muscle	Psoas
22	chr1:225677200-225703600	Weak transcription	Fetal Brain Female	brain
23	chr1:225679600-225696000	Weak transcription	Hela-S3	cervix
24	chr1:225680000-225690600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:225680200-225695600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:225680200-225696200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:225680800-225691000	Strong transcription	NH-A	brain
28	chr1:225680800-225696200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:225681200-225696200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:225681600-225688200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:225681800-225699800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:225682200-225688000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:225682200-225688400	Weak transcription	NHEK	skin
34	chr1:225683000-225696000	Weak transcription	HMEC	breast
35	chr1:225683000-225696800	Weak transcription	Lung	lung
36	chr1:225683200-225693800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:225683400-225693800	Weak transcription	Liver	Liver
38	chr1:225683400-225696600	Weak transcription	Right Ventricle	heart
39	chr1:225683800-225688200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:225684200-225688400	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr1:225684200-225696800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:225684400-225689400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:225684600-225688200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:225685400-225693600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr1:225685600-225694200	Weak transcription	Fetal Brain Male	brain
46	chr1:225686000-225689000	Strong transcription	A549	lung
47	chr1:225686200-225688200	Weak transcription	Fetal Intestine Large	intestine
48	chr1:225686200-225692600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:225686400-225693800	Weak transcription	Fetal Kidney	kidney
50	chr1:225686400-225693800	Weak transcription	HepG2	liver

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