Variant report

Variant	rs10260414
Chromosome Location	chr7:112118623-112118624
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	POLR2A	chr7:112116592-112118819	IMR90	lung:	n/a	n/a
2	POLR2A	chr7:112118525-112118853	GM12891	blood:	n/a	n/a
3	POLR2A	chr7:112116027-112120055	A549	lung:	n/a	n/a
4	POLR2A	chr7:112118608-112118906	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr7:112115869-112121327	K562	blood:	n/a	n/a
6	POLR2A	chr7:112118469-112118953	GM12878	blood:	n/a	n/a
7	POLR2A	chr7:112115373-112119161	HepG2	liver:	n/a	n/a
8	POLR2A	chr7:112118610-112118748	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:112088943..112098465-chr7:112111106..112127214,31	K562	blood:
2	chr7:112117720..112119517-chr7:112121271..112122829,2	K562	blood:
3	chr7:112113015..112114902-chr7:112118169..112120483,2	MCF-7	breast:

Variant related genes	Relation type
LSMEM1	TF binding region
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1005659	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1005661	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1024568	1.00[ASN][1000 genomes]
rs1024569	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1024570	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1024572	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029631	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10500007	0.91[ASN][1000 genomes]
rs1054043	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953712	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10953713	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11514940	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764489	0.85[ASN][1000 genomes]
rs11769604	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12154294	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531101	0.86[ASN][1000 genomes]
rs12531636	0.86[ASN][1000 genomes]
rs12539263	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468457	1.00[ASN][1000 genomes]
rs1468458	1.00[ASN][1000 genomes]
rs17159684	0.95[ASN][1000 genomes]
rs17159686	1.00[ASN][1000 genomes]
rs1963308	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190587	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396541	0.99[ASN][1000 genomes]
rs2396542	1.00[ASN][1000 genomes]
rs3095025	0.91[AFR][1000 genomes]
rs3095035	1.00[ASN][1000 genomes]
rs34633971	1.00[ASN][1000 genomes]
rs36095669	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807206	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807210	1.00[ASN][1000 genomes]
rs3807213	1.00[ASN][1000 genomes]
rs4275157	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4727771	0.91[ASN][1000 genomes]
rs4727774	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730548	0.91[ASN][1000 genomes]
rs4730549	0.91[ASN][1000 genomes]
rs55954386	0.92[ASN][1000 genomes]
rs56020731	0.91[ASN][1000 genomes]
rs6944364	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6945176	0.92[ASN][1000 genomes]
rs6967593	0.92[ASN][1000 genomes]
rs6967894	0.92[ASN][1000 genomes]
rs6968084	0.92[ASN][1000 genomes]
rs6973615	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73201469	1.00[ASN][1000 genomes]
rs7455170	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7777925	1.00[ASN][1000 genomes]
rs7817	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10260414	IFRD1	Cis_1M	lymphoblastoid	RTeQTL
rs10260414	IFRD1	cis	Thyroid	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112092600-112121800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:112094000-112121400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:112095600-112118800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:112096400-112121600	Strong transcription	Liver	Liver
5	chr7:112096400-112121800	Weak transcription	Stomach Mucosa	stomach
6	chr7:112100600-112135000	Weak transcription	Esophagus	oesophagus
7	chr7:112102800-112119800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr7:112103000-112119600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr7:112103600-112121200	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr7:112103600-112121800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:112105600-112121800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr7:112107800-112120800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr7:112110600-112120400	Weak transcription	Fetal Heart	heart
14	chr7:112110600-112124600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:112111200-112127200	Weak transcription	Fetal Brain Male	brain
16	chr7:112111600-112122200	Weak transcription	Fetal Kidney	kidney
17	chr7:112112000-112120400	Weak transcription	Gastric	stomach
18	chr7:112112400-112119400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr7:112112400-112121800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr7:112112400-112122200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr7:112112600-112129000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr7:112112800-112120600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr7:112112800-112120600	Weak transcription	Brain Angular Gyrus	brain
24	chr7:112113200-112120200	Weak transcription	Psoas Muscle	Psoas
25	chr7:112113200-112122600	Weak transcription	Colonic Mucosa	Colon
26	chr7:112113200-112124600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr7:112113200-112124800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr7:112113200-112125000	Weak transcription	Right Ventricle	heart
29	chr7:112113400-112127600	Weak transcription	Spleen	Spleen
30	chr7:112114200-112120600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr7:112114400-112120200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr7:112114400-112120800	Weak transcription	Brain Hippocampus Middle	brain
33	chr7:112114400-112132000	Weak transcription	HepG2	liver
34	chr7:112114600-112119200	Weak transcription	Brain Germinal Matrix	brain
35	chr7:112114600-112121800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr7:112114600-112125000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:112116200-112118800	Weak transcription	Primary B cells from cord blood	blood
38	chr7:112116400-112120400	Weak transcription	NH-A	brain
39	chr7:112116400-112121000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:112116400-112122000	Weak transcription	Fetal Lung	lung
41	chr7:112116600-112119200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr7:112116600-112119400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr7:112116600-112120600	Weak transcription	Brain Anterior Caudate	brain
44	chr7:112116600-112120600	Weak transcription	Colon Smooth Muscle	Colon
45	chr7:112116600-112120600	Weak transcription	HMEC	breast
46	chr7:112116600-112122000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr7:112116800-112119000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr7:112116800-112120400	Weak transcription	HUVEC	blood vessel
49	chr7:112116800-112121200	Weak transcription	NHEK	skin
50	chr7:112116800-112132200	Weak transcription	Fetal Intestine Small	intestine

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