Variant report

Variant	rs1348798
Chromosome Location	chr8:117885717-117885718
allele	A/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	POLR2A	chr8:117885414-117886264	SK-N-MC	brain:	n/a	n/a
2	STAT3	chr8:117885689-117885931	MCF10A-Er-Src	breast:	n/a	chr8:117885848-117885856 chr8:117885846-117885857
3	POLR2A	chr8:117885541-117887651	GM12891	blood:	n/a	n/a
4	JUND	chr8:117885491-117886117	K562	blood:	n/a	n/a
5	ARID3A	chr8:117885466-117885734	K562	blood:	n/a	n/a
6	POLR2A	chr8:117885510-117887543	GM12878	blood:	n/a	n/a
7	HCFC1	chr8:117885500-117887725	Hela-S3	cervix:	n/a	n/a
8	SIN3A	chr8:117885516-117887245	H1-hESC	embryonic stem cell:	n/a	chr8:117886316-117886327 chr8:117886314-117886327 chr8:117886666-117886677
9	RELA	chr8:117885687-117886209	GM12878	blood:	n/a	n/a
10	CUX1	chr8:117885683-117886204	GM12878	blood:	n/a	n/a
11	CHD1	chr8:117885476-117886802	GM12878	blood:	n/a	n/a
12	POLR2A	chr8:117885337-117887395	Hela-S3	cervix:	n/a	n/a
13	EBF1	chr8:117885641-117887369	GM12878	blood:	n/a	chr8:117885924-117885935
14	SIN3AK20	chr8:117885527-117887516	MCF-7	breast:	n/a	n/a
15	POLR2A	chr8:117885510-117887472	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr8:117884534-117887510	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr8:117885606-117887533	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr8:117885496-117885973	GM12878	blood:	n/a	chr8:117885848-117885856 chr8:117885846-117885857
19	WRNIP1	chr8:117885629-117886112	GM12878	blood:	n/a	n/a
20	STAT3	chr8:117885657-117885935	MCF10A-Er-Src	breast:	n/a	chr8:117885848-117885856 chr8:117885846-117885857
21	IRF1	chr8:117884816-117886172	K562	blood:	n/a	n/a
22	CEBPB	chr8:117885248-117885756	K562	blood:	n/a	n/a
23	CHD1	chr8:117885417-117886594	H1-hESC	embryonic stem cell:	n/a	n/a
24	PML	chr8:117885614-117887492	GM12878	blood:	n/a	n/a
25	REST	chr8:117885701-117887811	H1-neurons	neurons:	n/a	chr8:117886314-117886327 chr8:117886270-117886283 chr8:117886311-117886324 chr8:117886957-117886967 chr8:117886375-117886393
26	NFIC	chr8:117885662-117886169	GM12878	blood:	n/a	n/a
27	POLR2A	chr8:117882604-117887373	K562	blood:	n/a	n/a
28	FOXM1	chr8:117885651-117886177	GM12878	blood:	n/a	n/a
29	MXI1	chr8:117885043-117887774	SK-N-SH	brain:	n/a	n/a
30	GATA1	chr8:117885394-117886168	PBDE	blood:	n/a	n/a
31	BRCA1	chr8:117884921-117885939	Hela-S3	cervix:	n/a	n/a
32	ZNF384	chr8:117885586-117886118	GM12878	blood:	n/a	n/a
33	TBP	chr8:117884862-117886182	Hela-S3	cervix:	n/a	n/a
34	TBL1XR1	chr8:117885234-117886162	K562	blood:	n/a	n/a
35	RELA	chr8:117885689-117887436	GM12891	blood:	n/a	n/a
36	ZNF384	chr8:117885382-117885985	K562	blood:	n/a	n/a
37	MXI1	chr8:117885400-117886115	GM12878	blood:	n/a	n/a
38	E2F4	chr8:117885210-117887482	MCF10A-Er-Src	breast:	n/a	chr8:117887100-117887109 chr8:117886962-117886972 chr8:117886749-117886761 chr8:117887147-117887156 chr8:117886719-117886734 chr8:117887281-117887290
39	RELA	chr8:117885716-117886643	GM19099	blood:	n/a	n/a
40	TBP	chr8:117885505-117886187	GM12878	blood:	n/a	n/a
41	CUX1	chr8:117885383-117886203	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:117777450..117780279-chr8:117883824..117887176,3	MCF-7	breast:
2	chr17:57182556..57185500-chr8:117885243..117887257,2	MCF-7	breast:
3	chr8:117766167..117768500-chr8:117885619..117887391,2	K562	blood:
4	chr5:108745137..108745914-chr8:117885074..117885909,2	Hela-S3	cervix:
5	chr8:117776578..117778707-chr8:117885688..117887716,2	MCF-7	breast:
6	chr8:117860936..117862672-chr8:117885542..117887768,2	MCF-7	breast:
7	chr12:120517214..120519596-chr8:117884799..117887415,2	MCF-7	breast:
8	chr8:117777051..117780452-chr8:117884154..117888588,6	K562	blood:

Variant related genes	Relation type
RAD21-AS1	TF binding region
ENSG00000147679	Chromatin interaction
ENSG00000224738	Chromatin interaction
ENSG00000198961	Chromatin interaction
ENSG00000147677	Chromatin interaction
ENSG00000135127	Chromatin interaction
ENSG00000108395	Chromatin interaction
ENSG00000164754	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12547184	1.00[YRI][hapmap]
rs12549895	1.00[YRI][hapmap]
rs1348795	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1374295	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17744897	1.00[YRI][hapmap]
rs17812479	1.00[YRI][hapmap]
rs3020117	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020129	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7824338	0.91[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530386	chr8:117509968-118391406	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv831434	chr8:117784467-117977825	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv891407	chr8:117881393-117895239	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
4	nsv891408	chr8:117884270-117895239	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1348798	RAD21	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:117860400-117885800	Weak transcription	Esophagus	oesophagus
2	chr8:117864400-117885800	Weak transcription	Gastric	stomach
3	chr8:117865200-117885800	Weak transcription	Pancreas	Pancrea
4	chr8:117865600-117885800	Weak transcription	Spleen	Spleen
5	chr8:117878800-117885800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr8:117881200-117887800	Active TSS	GM12878-XiMat	blood
7	chr8:117881800-117885800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr8:117882600-117885800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:117883200-117885800	Weak transcription	Lung	lung
10	chr8:117883600-117887600	Active TSS	HSMMtube	muscle
11	chr8:117884000-117886000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr8:117884000-117887800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr8:117884000-117887800	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr8:117884200-117887600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr8:117884200-117887600	Active TSS	K562	blood
16	chr8:117884400-117885800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr8:117884400-117885800	Flanking Active TSS	HUVEC	blood vessel
18	chr8:117884400-117887600	Active TSS	Thymus	Thymus
19	chr8:117884400-117887800	Active TSS	A549	lung
20	chr8:117884600-117885800	Flanking Active TSS	Liver	Liver
21	chr8:117884600-117885800	Flanking Active TSS	Osteobl	bone
22	chr8:117884600-117886000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr8:117884600-117886000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr8:117884600-117886200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr8:117884600-117886200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr8:117884600-117886200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr8:117884600-117887400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr8:117884600-117887400	Active TSS	Hela-S3	cervix
29	chr8:117884600-117887600	Active TSS	H1 Cell Line	embryonic stem cell
30	chr8:117884600-117887600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr8:117884600-117887600	Active TSS	Aorta	Aorta
32	chr8:117884600-117887600	Active TSS	Fetal Muscle Trunk	muscle
33	chr8:117884600-117887600	Active TSS	Right Atrium	heart
34	chr8:117884600-117887600	Active TSS	HSMM	muscle
35	chr8:117884600-117887800	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr8:117884800-117885800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr8:117884800-117885800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr8:117884800-117886000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr8:117884800-117886000	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr8:117884800-117886200	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr8:117884800-117886400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr8:117884800-117887400	Active TSS	H9 Cell Line	embryonic stem cell
43	chr8:117884800-117887600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr8:117884800-117887600	Active TSS	Primary T cells fromperipheralblood	blood
45	chr8:117884800-117887600	Active TSS	Fetal Intestine Large	intestine
46	chr8:117884800-117887600	Active TSS	Fetal Thymus	thymus
47	chr8:117884800-117887600	Active TSS	Right Ventricle	heart
48	chr8:117884800-117887800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr8:117885000-117885800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr8:117885000-117885800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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