Variant report

Variant	rs35394459
Chromosome Location	chr10:112625677-112625678
allele	C/G/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	SPI1	chr10:112625405-112625780	GM12891	blood:	n/a	n/a
2	STAT5A	chr10:112625667-112626181	GM12878	blood:	n/a	n/a
3	ZNF384	chr10:112624243-112625994	GM12878	blood:	n/a	n/a
4	RELA	chr10:112625400-112626103	GM18951	blood:	n/a	n/a
5	STAT1	chr10:112625189-112626229	Hela-S3	cervix:	n/a	n/a
6	SPI1	chr10:112625403-112625724	GM12878	blood:	n/a	n/a
7	TBP	chr10:112625233-112626129	Hela-S3	cervix:	n/a	n/a
8	SP1	chr10:112625002-112625763	A549	lung:	n/a	chr10:112625269-112625278 chr10:112625268-112625280
9	CEBPB	chr10:112625420-112625727	A549	lung:	n/a	chr10:112625499-112625510
10	RELA	chr10:112625103-112626409	GM19099	blood:	n/a	n/a
11	POLR2A	chr10:112623930-112626260	GM12891	blood:	n/a	n/a
12	EBF1	chr10:112625475-112625797	GM12878	blood:	n/a	n/a
13	EP300	chr10:112625391-112625950	GM12878	blood:	n/a	n/a
14	NFIC	chr10:112625039-112626080	GM12878	blood:	n/a	n/a
15	PML	chr10:112625279-112626577	GM12878	blood:	n/a	n/a
16	ATF2	chr10:112625446-112626022	GM12878	blood:	n/a	n/a
17	RELA	chr10:112625251-112626367	GM12878	blood:	n/a	n/a
18	FOXM1	chr10:112625328-112626202	GM12878	blood:	n/a	n/a
19	ATF2	chr10:112625394-112625936	GM12878	blood:	n/a	n/a
20	MTA3	chr10:112625026-112626353	GM12878	blood:	n/a	n/a
21	RUNX3	chr10:112625309-112626109	GM12878	blood:	n/a	n/a
22	FOSL1	chr10:112625005-112626285	HCT-116	colon:	n/a	chr10:112625325-112625337
23	RCOR1	chr10:112625472-112626299	GM12878	blood:	n/a	n/a
24	SMC3	chr10:112625239-112626225	GM12878	blood:	n/a	n/a
25	TBP	chr10:112625401-112626150	GM12878	blood:	n/a	n/a
26	RELA	chr10:112625437-112626237	GM12891	blood:	n/a	n/a
27	NFIC	chr10:112625280-112626249	GM12878	blood:	n/a	n/a
28	CHD1	chr10:112625107-112626009	GM12878	blood:	n/a	n/a
29	FOSL2	chr10:112625120-112625740	A549	lung:	n/a	chr10:112625325-112625337
30	TBL1XR1	chr10:112625456-112626038	GM12878	blood:	n/a	n/a
31	TCF12	chr10:112625156-112625759	A549	lung:	n/a	chr10:112625304-112625314
32	BCLAF1	chr10:112625379-112626177	GM12878	blood:	n/a	chr10:112625680-112625689 chr10:112625681-112625690 chr10:112626008-112626017
33	RUNX3	chr10:112625325-112626129	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:112610748..112613703-chr10:112623981..112626805,2	MCF-7	breast:
2	chr10:112532259..112533809-chr10:112624072..112626990,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232470	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10082499	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10787286	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10787291	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10787293	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10885059	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885060	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885061	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10885064	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10885071	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10885076	0.81[EUR][1000 genomes]
rs11195361	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11195366	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11195381	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11195387	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11195390	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11195398	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12240685	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12242177	0.81[AFR][1000 genomes]
rs12242928	0.81[AFR][1000 genomes]
rs12258559	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12261765	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12776359	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12776861	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2146544	0.83[AFR][1000 genomes]
rs34401279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34893229	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35793075	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35946882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750619	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3763692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4917589	0.86[ASN][1000 genomes]
rs6585026	0.81[EUR][1000 genomes]
rs7089687	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7919142	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045608	chr10:112524813-112677557	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1041758	chr10:112552897-112677557	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv896003	chr10:112579299-112631211	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv896002	chr10:112579299-112638028	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35394459	LOC92482	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112611200-112630600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:112617000-112628600	Enhancers	Placenta	Placenta
3	chr10:112617800-112630600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:112618400-112630800	Enhancers	Fetal Thymus	thymus
5	chr10:112619800-112627400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr10:112621000-112630600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:112621000-112631000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr10:112621200-112630400	Weak transcription	Gastric	stomach
9	chr10:112621200-112630600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr10:112621200-112630600	Weak transcription	Brain Substantia Nigra	brain
11	chr10:112621800-112628600	Enhancers	Fetal Muscle Leg	muscle
12	chr10:112622000-112626200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr10:112622000-112628400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr10:112622200-112626400	Enhancers	Fetal Stomach	stomach
15	chr10:112622200-112628400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr10:112623000-112630600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr10:112623200-112628200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr10:112623400-112627600	Enhancers	Fetal Intestine Small	intestine
19	chr10:112623400-112631000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr10:112623600-112627400	Enhancers	Fetal Muscle Trunk	muscle
21	chr10:112623800-112626000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr10:112623800-112626200	Enhancers	Fetal Lung	lung
23	chr10:112623800-112628400	Enhancers	Small Intestine	intestine
24	chr10:112624000-112626200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr10:112624000-112626200	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr10:112624000-112627800	Enhancers	Fetal Intestine Large	intestine
27	chr10:112624000-112627800	Enhancers	Stomach Mucosa	stomach
28	chr10:112624000-112630600	Weak transcription	Lung	lung
29	chr10:112624200-112626000	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr10:112624200-112626400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr10:112624200-112628200	Enhancers	HSMM	muscle
32	chr10:112624400-112626000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr10:112624400-112626000	Enhancers	Right Atrium	heart
34	chr10:112624400-112626000	Enhancers	NHLF	lung
35	chr10:112624400-112626200	Enhancers	Esophagus	oesophagus
36	chr10:112624400-112626200	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr10:112624400-112626200	Enhancers	Stomach Smooth Muscle	stomach
38	chr10:112624400-112626200	Enhancers	Osteobl	bone
39	chr10:112624400-112626400	Enhancers	HMEC	breast
40	chr10:112624400-112627000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr10:112624400-112627200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr10:112624400-112628400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr10:112624400-112628400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr10:112624400-112628600	Enhancers	Placenta Amnion	Placenta Amnion
45	chr10:112624600-112625800	Enhancers	Colon Smooth Muscle	Colon
46	chr10:112624600-112626000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr10:112624600-112626000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr10:112624600-112626000	Flanking Active TSS	A549	lung
49	chr10:112624600-112626000	Flanking Active TSS	Hela-S3	cervix
50	chr10:112624600-112626200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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