Variant report

Variant	rs3807213
Chromosome Location	chr7:112105754-112105755
allele	A/C
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	POLR2A	chr7:112098412-112105971	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:112088811..112094041-chr7:112100770..112110657,18	MCF-7	breast:
2	chr7:112100687..112102233-chr7:112105743..112108488,2	MCF-7	breast:

Variant related genes	Relation type
IFRD1	TF binding region
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1005659	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1005661	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1024568	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1024569	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1024570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1024572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10260414	1.00[ASN][1000 genomes]
rs1029631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10500007	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs1054043	1.00[ASN][1000 genomes]
rs10953712	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10953713	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11514940	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11764489	0.85[ASN][1000 genomes]
rs11769604	0.99[ASN][1000 genomes]
rs12154294	1.00[ASN][1000 genomes]
rs12531101	0.86[ASN][1000 genomes]
rs12531636	0.86[ASN][1000 genomes]
rs12539263	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1468457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17159684	0.95[ASN][1000 genomes]
rs17159686	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1963308	1.00[ASN][1000 genomes]
rs2074796	0.81[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs2190587	1.00[ASN][1000 genomes]
rs2253962	1.00[LWK][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs2396541	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2396542	1.00[ASN][1000 genomes]
rs2708611	0.91[YRI][hapmap]
rs3095035	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3128386	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs3128388	0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs34633971	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36095669	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3807206	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3807210	1.00[ASN][1000 genomes]
rs4275157	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4386904	0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs4727771	0.91[ASN][1000 genomes]
rs4727774	1.00[ASN][1000 genomes]
rs4730548	0.91[ASN][1000 genomes]
rs4730549	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs55954386	0.92[ASN][1000 genomes]
rs56020731	0.91[ASN][1000 genomes]
rs6944364	1.00[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6945176	0.92[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs6963343	0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs6966318	1.00[LWK][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs6967593	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[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6967894	0.92[ASN][1000 genomes]
rs6968084	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6973615	1.00[ASN][1000 genomes]
rs73201469	1.00[ASN][1000 genomes]
rs7455170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7467	0.81[ASW][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7777925	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7817	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[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	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	nsv831097	chr7:112000837-112113173	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1030033	chr7:112092709-112140430	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3807213	LSMEM1	cis	Thyroid	GTEx
rs3807213	IFRD1	cis	Esophagus Mucosa	GTEx
rs3807213	C7orf53	cis	cerebellum	SCAN
rs3807213	IFRD1	cis	Thyroid	GTEx
rs3807213	IFRD1	Cis_1M	lymphoblastoid	RTeQTL
rs3807213	IFRD1	cis	parietal	SCAN
rs3807213	C7orf53	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112092600-112109800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:112092600-112121800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:112093000-112109600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:112094000-112118200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:112094000-112121400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:112094400-112118200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr7:112094600-112109800	Weak transcription	Small Intestine	intestine
8	chr7:112094600-112114800	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:112094600-112117000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:112095000-112114200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:112095200-112109800	Weak transcription	Right Ventricle	heart
12	chr7:112095200-112117400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr7:112095400-112108000	Strong transcription	Fetal Intestine Large	intestine
14	chr7:112095400-112117200	Strong transcription	Dnd41	blood
15	chr7:112095600-112116400	Strong transcription	NH-A	brain
16	chr7:112095600-112116600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr7:112095600-112117200	Strong transcription	HSMM	muscle
18	chr7:112095600-112117400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr7:112095600-112117400	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr7:112095600-112117400	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr7:112095600-112118800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:112095800-112114600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr7:112095800-112117000	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr7:112095800-112117000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr7:112095800-112117400	Strong transcription	Fetal Thymus	thymus
26	chr7:112095800-112118000	Strong transcription	Placenta	Placenta
27	chr7:112095800-112118200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr7:112095800-112118200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:112096000-112105800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr7:112096000-112105800	Strong transcription	HepG2	liver
31	chr7:112096000-112116800	Strong transcription	HUVEC	blood vessel
32	chr7:112096200-112107000	Strong transcription	GM12878-XiMat	blood
33	chr7:112096400-112121600	Strong transcription	Liver	Liver
34	chr7:112096400-112121800	Weak transcription	Stomach Mucosa	stomach
35	chr7:112096800-112117600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr7:112097800-112111400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr7:112100400-112108800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr7:112100600-112108000	Weak transcription	Fetal Intestine Small	intestine
39	chr7:112100600-112108000	Weak transcription	Fetal Stomach	stomach
40	chr7:112100600-112109200	Weak transcription	Gastric	stomach
41	chr7:112100600-112109400	Weak transcription	Lung	lung
42	chr7:112100600-112109400	Weak transcription	Ovary	ovary
43	chr7:112100600-112109600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:112100600-112109600	Weak transcription	Aorta	Aorta
45	chr7:112100600-112111000	Weak transcription	Spleen	Spleen
46	chr7:112100600-112112800	Weak transcription	Pancreas	Pancrea
47	chr7:112100600-112135000	Weak transcription	Esophagus	oesophagus
48	chr7:112100800-112105800	Strong transcription	NHLF	lung
49	chr7:112101000-112114400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr7:112101000-112118000	Strong transcription	Rectal Mucosa Donor 29	rectum

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