Variant report

Variant	rs6984959
Chromosome Location	chr8:90915464-90915465
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	chr8:90913673-90916136	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr8:90914003-90915479	H1-hESC	embryonic stem cell:	n/a	n/a
3	CHD2	chr8:90914018-90915589	GM12878	blood:	n/a	chr8:90914652-90914662
4	RUNX3	chr8:90914915-90915652	GM12878	blood:	n/a	n/a
5	SIN3AK20	chr8:90913437-90915573	MCF-7	breast:	n/a	n/a
6	USF1	chr8:90915112-90915499	ECC-1	luminal epithelium:	n/a	n/a
7	TBP	chr8:90915312-90915502	GM12878	blood:	n/a	n/a
8	MAZ	chr8:90913904-90915548	K562	blood:	n/a	chr8:90914898-90914908 chr8:90915180-90915190
9	POLR2A	chr8:90913746-90915727	GM12891	blood:	n/a	n/a
10	MXI1	chr8:90913464-90915946	SK-N-SH	brain:	n/a	n/a
11	MYC	chr8:90913767-90915566	K562	blood:	n/a	chr8:90914898-90914908 chr8:90915180-90915190
12	RUNX3	chr8:90913884-90915486	GM12878	blood:	n/a	n/a
13	SMC3	chr8:90915462-90915521	GM12878	blood:	n/a	n/a
14	POLR2A	chr8:90913891-90915474	GM18505	blood:	n/a	n/a
15	SPI1	chr8:90914987-90915492	HL-60	blood:	n/a	chr8:90915262-90915275
16	POLR2A	chr8:90913915-90915926	GM12878	blood:	n/a	n/a
17	BHLHE40	chr8:90914091-90915501	HepG2	liver:	n/a	chr8:90914721-90914737 chr8:90914735-90914751 chr8:90914729-90914745
18	CHD2	chr8:90914193-90915511	K562	blood:	n/a	chr8:90914652-90914662
19	POLR2A	chr8:90915419-90915570	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr8:90914431-90915615	IMR90	lung:	n/a	n/a
21	IRF1	chr8:90915406-90915577	K562	blood:	n/a	n/a
22	USF1	chr8:90915153-90915519	H1-hESC	embryonic stem cell:	n/a	n/a
23	USF1	chr8:90915124-90915512	K562	blood:	n/a	n/a
24	MAX	chr8:90912888-90915495	MCF-7	breast:	n/a	chr8:90914898-90914908 chr8:90915180-90915190
25	STAT3	chr8:90915373-90915596	GM12878	blood:	n/a	n/a
26	EP300	chr8:90915304-90915519	GM12878	blood:	n/a	n/a
27	POLR2A	chr8:90913927-90915546	HL-60	blood:	n/a	n/a
28	POLR2A	chr8:90913901-90915565	GM19099	blood:	n/a	n/a
29	MAZ	chr8:90913888-90915564	IMR90	lung:	n/a	chr8:90914898-90914908 chr8:90915180-90915190
30	MAX	chr8:90913899-90915557	NB4	blood:	n/a	chr8:90914898-90914908 chr8:90915180-90915190
31	BHLHE40	chr8:90913874-90915718	GM12878	blood:	n/a	chr8:90914721-90914737 chr8:90914735-90914751 chr8:90914729-90914745
32	POLR2A	chr8:90913876-90916292	Hela-S3	cervix:	n/a	n/a
33	BRCA1	chr8:90915213-90915738	H1-hESC	embryonic stem cell:	n/a	n/a
34	MYC	chr8:90913882-90915477	NB4	blood:	n/a	chr8:90914898-90914908 chr8:90915180-90915190
35	JUND	chr8:90913580-90915681	K562	blood:	n/a	chr8:90914754-90914763
36	POLR2A	chr8:90913873-90915509	GM12892	blood:	n/a	n/a
37	CHD1	chr8:90914346-90915903	H1-hESC	embryonic stem cell:	n/a	chr8:90914652-90914662
38	POLR2A	chr8:90913849-90915509	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr8:90914001-90915491	ProgFib	skin:	n/a	n/a
40	EP300	chr8:90914026-90915567	GM12878	blood:	n/a	chr8:90914538-90914554 chr8:90914701-90914717 chr8:90914722-90914738
41	BACH1	chr8:90915306-90915530	H1-hESC	embryonic stem cell:	n/a	n/a
42	HA-E2F1	chr8:90912833-90915523	MCF-7	breast:	n/a	chr8:90914540-90914549 chr8:90914800-90914810 chr8:90914874-90914884 chr8:90914760-90914769
43	RCOR1	chr8:90914283-90915531	GM12878	blood:	n/a	n/a
44	UBTF	chr8:90913917-90915470	K562	blood:	n/a	n/a
45	BHLHE40	chr8:90914023-90915556	K562	blood:	n/a	chr8:90914721-90914737 chr8:90914735-90914751 chr8:90914729-90914745
46	POLR2A	chr8:90913769-90915508	GM12878	blood:	n/a	n/a
47	SIN3AK20	chr8:90912996-90915794	MCF-7	breast:	n/a	n/a
48	HDAC2	chr8:90913295-90915500	MCF-7	breast:	n/a	chr8:90913650-90913664
49	POLR2A	chr8:90913764-90916967	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr8:90913973-90915541	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:90913376..90915525-chr8:90949213..90951083,2	K562	blood:
2	chr8:90767168..90772413-chr8:90911120..90917480,11	K562	blood:
3	chr8:90914281..90916675-chr8:91011002..91013854,2	MCF-7	breast:
4	chr8:90767236..90773457-chr8:90912212..90919638,16	MCF-7	breast:
5	chr8:90913353..90915903-chr8:90994626..90998419,6	K562	blood:
6	chr8:90854578..90857222-chr8:90915273..90917997,2	MCF-7	breast:
7	chr8:90914226..90916241-chr8:91996581..91998635,2	K562	blood:
8	chr8:90911185..90916499-chr8:90992960..90998209,20	MCF-7	breast:
9	chr8:90766999..90771986-chr8:90912842..90916534,13	MCF-7	breast:
10	chr8:90913046..90917912-chr8:90949306..90952418,7	MCF-7	breast:
11	chr8:90915281..90919071-chr8:91010882..91014336,4	MCF-7	breast:
12	chr8:90912595..90916756-chr8:90994852..90998205,9	K562	blood:
13	chr8:90913489..90916241-chr8:91996581..91998462,2	K562	blood:
14	chr8:90914455..90916377-chr8:91657322..91659594,2	K562	blood:
15	chr8:90913007..90918207-chr8:90995257..90997906,9	MCF-7	breast:

Variant related genes	Relation type
RNU6-925P	TF binding region
ENSG00000246792	Chromatin interaction
ENSG00000104312	Chromatin interaction
ENSG00000180694	Chromatin interaction
ENSG00000251136	Chromatin interaction
ENSG00000104320	Chromatin interaction
ENSG00000104325	Chromatin interaction
ENSG00000253250	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10091400	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10102707	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1024156	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11992886	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13312973	1.00[ASN][1000 genomes]
rs13312981	1.00[ASN][1000 genomes]
rs13312987	1.00[ASN][1000 genomes]
rs16901426	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16901712	1.00[ASN][1000 genomes]
rs28488469	1.00[ASN][1000 genomes]
rs28533586	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28578207	1.00[ASN][1000 genomes]
rs62531975	0.83[ASN][1000 genomes]
rs62531976	0.83[ASN][1000 genomes]
rs62531977	0.83[ASN][1000 genomes]
rs62531978	0.83[ASN][1000 genomes]
rs6470477	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6986890	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6994296	0.82[AMR][1000 genomes]
rs6998717	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6998735	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7000851	1.00[ASN][1000 genomes]
rs7001024	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7004247	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7004411	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7004759	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7005165	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73696831	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7828593	1.00[ASN][1000 genomes]
rs7829683	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs983925	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][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	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	esv3371037	chr8:90912579-90917077	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	esv3328681	chr8:90913579-90916277	Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	esv3321826	chr8:90913604-90916152	Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90912800-90916200	Active TSS	A549	lung
2	chr8:90913200-90916000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr8:90913200-90917200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr8:90913400-90915600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr8:90913400-90915600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr8:90913400-90916200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr8:90913400-90916200	Active TSS	HSMMtube	muscle
8	chr8:90913400-90916400	Active TSS	H1 Cell Line	embryonic stem cell
9	chr8:90913400-90916400	Active TSS	Brain Substantia Nigra	brain
10	chr8:90913400-90916600	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr8:90913400-90916800	Active TSS	Brain Anterior Caudate	brain
12	chr8:90913600-90915600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr8:90913600-90915600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr8:90913600-90915600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr8:90913600-90915600	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr8:90913600-90915600	Active TSS	Rectal Mucosa Donor 31	rectum
17	chr8:90913600-90915800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr8:90913600-90916000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr8:90913600-90916000	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr8:90913600-90916000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr8:90913600-90916000	Active TSS	GM12878-XiMat	blood
22	chr8:90913600-90916200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr8:90913600-90916200	Active TSS	Fetal Kidney	kidney
24	chr8:90913600-90916400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr8:90913600-90916600	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr8:90913600-90916600	Active TSS	Rectal Smooth Muscle	rectum
27	chr8:90913600-90916600	Active TSS	K562	blood
28	chr8:90913600-90916800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr8:90913600-90917000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr8:90913600-90917000	Active TSS	Stomach Smooth Muscle	stomach
31	chr8:90913800-90915600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr8:90913800-90915600	Active TSS	Brain Hippocampus Middle	brain
33	chr8:90913800-90915600	Active TSS	Colonic Mucosa	Colon
34	chr8:90913800-90915600	Active TSS	Psoas Muscle	Psoas
35	chr8:90913800-90915600	Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr8:90913800-90915600	Active TSS	Stomach Mucosa	stomach
37	chr8:90913800-90915800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr8:90913800-90915800	Active TSS	H9 Cell Line	embryonic stem cell
39	chr8:90913800-90915800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr8:90913800-90915800	Active TSS	Fetal Brain Female	brain
41	chr8:90913800-90915800	Active TSS	Fetal Intestine Large	intestine
42	chr8:90913800-90915800	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr8:90913800-90915800	Active TSS	Right Ventricle	heart
44	chr8:90913800-90915800	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr8:90913800-90915800	Active TSS	Thymus	Thymus
46	chr8:90913800-90915800	Active TSS	HSMM	muscle
47	chr8:90913800-90916000	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr8:90913800-90916000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr8:90913800-90916000	Active TSS	HepG2	liver
50	chr8:90913800-90916400	Active TSS	Colon Smooth Muscle	Colon

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