Variant report

Variant	rs10882379
Chromosome Location	chr10:95751499-95751500
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	EP300	chr10:95750788-95752085	T-47D	breast:	n/a	chr10:95751987-95751996 chr10:95751988-95751997
2	REST	chr10:95751453-95752632	A549	lung:	n/a	n/a
3	FOSL1	chr10:95751485-95752273	HCT-116	colon:	n/a	chr10:95751988-95751995 chr10:95751987-95751997 chr10:95751987-95751996 chr10:95751988-95751996
4	NFIC	chr10:95751404-95752130	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr10:95751376-95752021	PANC-1	pancreas:	n/a	n/a
6	TCF12	chr10:95751319-95752291	A549	lung:	n/a	n/a
7	RAD21	chr10:95751411-95752124	A549	lung:	n/a	n/a
8	YY1	chr10:95751401-95751961	A549	lung:	n/a	n/a
9	E2F6	chr10:95751485-95752063	A549	lung:	n/a	n/a
10	MAX	chr10:95751485-95752180	ECC-1	luminal epithelium:	n/a	chr10:95751988-95751997 chr10:95751987-95751996
11	TCF7L2	chr10:95751475-95751855	PANC-1	pancreas:	n/a	n/a
12	YY1	chr10:95751447-95751635	HepG2	liver:	n/a	n/a
13	MAX	chr10:95751383-95752145	ECC-1	luminal epithelium:	n/a	chr10:95751988-95751997 chr10:95751987-95751996
14	MAX	chr10:95751474-95752593	A549	lung:	n/a	chr10:95751988-95751997 chr10:95751987-95751996
15	TEAD4	chr10:95751410-95752106	ECC-1	luminal epithelium:	n/a	n/a
16	JUND	chr10:95751452-95752294	SK-N-SH	brain:	n/a	chr10:95751988-95751995 chr10:95751987-95751997 chr10:95751987-95751996 chr10:95751988-95751996
17	MAX	chr10:95751360-95754515	A549	lung:	n/a	chr10:95751988-95751997 chr10:95751987-95751996
18	SP1	chr10:95751410-95752210	A549	lung:	n/a	chr10:95751895-95751902
19	NR3C1	chr10:95751436-95752015	A549	lung:	n/a	chr10:95751634-95751647
20	YY1	chr10:95751413-95751999	ECC-1	luminal epithelium:	n/a	n/a
21	E2F6	chr10:95751453-95752201	A549	lung:	n/a	n/a
22	KAP1	chr10:95751439-95752053	U2OS	brain:	n/a	chr10:95751986-95751995
23	JUND	chr10:95751464-95752214	T-47D	breast:	n/a	chr10:95751988-95751995 chr10:95751987-95751997 chr10:95751987-95751996 chr10:95751988-95751996
24	EP300	chr10:95751320-95752066	ECC-1	luminal epithelium:	n/a	chr10:95751987-95751996 chr10:95751988-95751997
25	TEAD4	chr10:95751373-95752100	ECC-1	luminal epithelium:	n/a	n/a
26	TEAD4	chr10:95751462-95752090	A549	lung:	n/a	n/a
27	FOSL2	chr10:95751327-95752556	A549	lung:	n/a	chr10:95751988-95751995 chr10:95751987-95751997 chr10:95751987-95751996 chr10:95751988-95751996
28	CEBPB	chr10:95751464-95752089	IMR90	lung:	n/a	n/a
29	JUND	chr10:95751447-95752294	SK-N-SH	brain:	n/a	chr10:95751988-95751995 chr10:95751987-95751997 chr10:95751987-95751996 chr10:95751988-95751996
30	KAP1	chr10:95751448-95752018	HEK293	kidney:	n/a	chr10:95751986-95751995
31	EP300	chr10:95751462-95752474	A549	lung:	n/a	chr10:95751987-95751996 chr10:95751988-95751997
32	MAFK	chr10:95751467-95751912	IMR90	lung:	n/a	chr10:95751798-95751813
33	JUND	chr10:95751436-95752341	SK-N-SH	brain:	n/a	chr10:95751988-95751995 chr10:95751987-95751997 chr10:95751987-95751996 chr10:95751988-95751996
34	SP1	chr10:95751318-95752541	A549	lung:	n/a	chr10:95751895-95751902
35	YY1	chr10:95751383-95752073	ECC-1	luminal epithelium:	n/a	n/a
36	EP300	chr10:95751348-95752144	A549	lung:	n/a	chr10:95751987-95751996 chr10:95751988-95751997
37	GATA3	chr10:95751366-95752153	T-47D	breast:	n/a	chr10:95751498-95751510
38	POLR2A	chr10:95751395-95753235	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr10:95751445-95751980	ECC-1	luminal epithelium:	n/a	n/a
40	TCF12	chr10:95751329-95752267	ECC-1	luminal epithelium:	n/a	n/a
41	NR3C1	chr10:95751497-95752043	ECC-1	luminal epithelium:	n/a	chr10:95751634-95751647

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:95735923..95738579-chr10:95750156..95752956,2	MCF-7	breast:

Variant related genes	Relation type
PLCE1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10882378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882380	1.00[ASW][hapmap];0.82[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11187741	0.89[ASN][1000 genomes]
rs11187760	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11187765	0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11187767	0.82[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11187789	1.00[LWK][hapmap]
rs11594479	0.89[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11599672	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12573786	0.89[ASN][1000 genomes]
rs17415514	1.00[LWK][hapmap];0.85[MKK][hapmap]
rs17415646	1.00[LWK][hapmap]
rs17506505	1.00[LWK][hapmap]
rs2182093	1.00[LWK][hapmap];0.85[MKK][hapmap]
rs35038192	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3814689	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61866000	0.89[ASN][1000 genomes]
rs61866026	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61886277	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6583922	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7071652	0.82[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7073291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094594	0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038218	chr10:95728508-95751499	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10882379	ALDH18A1	cis	parietal	SCAN
rs10882379	ANKRD2	cis	parietal	SCAN
rs10882379	PLCE1	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:95750000-95753200	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr10:95750400-95751600	Enhancers	Fetal Muscle Leg	muscle
3	chr10:95750400-95753000	Enhancers	Brain Germinal Matrix	brain
4	chr10:95750400-95753000	Enhancers	Fetal Stomach	stomach
5	chr10:95750400-95753000	Enhancers	Stomach Mucosa	stomach
6	chr10:95750400-95753200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr10:95750600-95751600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr10:95750600-95751600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr10:95750600-95751600	Enhancers	HSMM	muscle
10	chr10:95750600-95752000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr10:95750600-95752000	Enhancers	Hela-S3	cervix
12	chr10:95750600-95752000	Enhancers	HSMMtube	muscle
13	chr10:95750600-95752400	Enhancers	HepG2	liver
14	chr10:95750600-95752600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr10:95750600-95752800	Enhancers	Fetal Brain Female	brain
16	chr10:95750600-95753000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr10:95750600-95753000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr10:95750600-95753000	Enhancers	Fetal Heart	heart
19	chr10:95750600-95753200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr10:95750600-95753200	Enhancers	Fetal Intestine Small	intestine
21	chr10:95750800-95751600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr10:95750800-95751600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr10:95750800-95751600	Enhancers	Right Ventricle	heart
24	chr10:95750800-95751600	Enhancers	NHLF	lung
25	chr10:95750800-95751800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr10:95750800-95752000	Bivalent Enhancer	Brain Cingulate Gyrus	brain
27	chr10:95750800-95752000	Flanking Active TSS	A549	lung
28	chr10:95750800-95752400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
29	chr10:95750800-95752400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr10:95750800-95752600	Enhancers	Duodenum Mucosa	Duodenum
31	chr10:95750800-95752600	Enhancers	Stomach Smooth Muscle	stomach
32	chr10:95750800-95752800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr10:95750800-95752800	Enhancers	Brain Hippocampus Middle	brain
34	chr10:95750800-95753000	Enhancers	Fetal Intestine Large	intestine
35	chr10:95750800-95753000	Enhancers	Left Ventricle	heart
36	chr10:95750800-95753000	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr10:95750800-95753000	Enhancers	Right Atrium	heart
38	chr10:95750800-95753000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr10:95751000-95751600	Enhancers	Adipose Nuclei	Adipose
40	chr10:95751000-95751800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr10:95751000-95751800	Weak transcription	Lung	lung
42	chr10:95751000-95752000	Enhancers	Brain Anterior Caudate	brain
43	chr10:95751000-95752000	Enhancers	Ovary	ovary
44	chr10:95751000-95752400	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr10:95751000-95752600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr10:95751000-95752600	Weak transcription	Fetal Brain Male	brain
47	chr10:95751000-95752600	Weak transcription	Gastric	stomach
48	chr10:95751000-95752600	Enhancers	HMEC	breast
49	chr10:95751000-95753000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
50	chr10:95751000-95753000	Weak transcription	Colonic Mucosa	Colon

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