Variant report

Variant	rs17249855
Chromosome Location	chr6:24666353-24666354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT1	chr6:24666149-24667614	GM12878	blood:	n/a	n/a
2	UBTF	chr6:24666205-24668049	K562	blood:	n/a	n/a
3	POLR2A	chr6:24666311-24667878	PBDE	blood:	n/a	n/a
4	SIN3A	chr6:24666296-24667709	H1-hESC	embryonic stem cell:	n/a	n/a
5	MYBL2	chr6:24666323-24668169	HepG2	liver:	n/a	n/a
6	ELK1	chr6:24666321-24667855	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr6:24666280-24666430	GM12871	blood:	n/a	n/a
8	TBL1XR1	chr6:24666246-24667669	K562	blood:	n/a	n/a
9	POLR2A	chr6:24666321-24667789	SK-N-MC	brain:	n/a	n/a
10	JUN	chr6:24665793-24668258	K562	blood:	n/a	n/a
11	POLR2A	chr6:24666241-24669322	Hela-S3	cervix:	n/a	n/a
12	IRF1	chr6:24666315-24668038	K562	blood:	n/a	chr6:24667614-24667625
13	GTF2F1	chr6:24666217-24667794	Hela-S3	cervix:	n/a	n/a
14	MTA3	chr6:24666327-24667746	GM12878	blood:	n/a	n/a
15	RCOR1	chr6:24666255-24667919	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr6:24666238-24667841	GM12878	blood:	n/a	n/a
17	MAX	chr6:24666308-24668110	HepG2	liver:	n/a	n/a
18	SMARCC1	chr6:24666319-24668171	Hela-S3	cervix:	n/a	n/a
19	ELF1	chr6:24666346-24667476	GM12878	blood:	n/a	chr6:24666898-24666907 chr6:24666897-24666906
20	REST	chr6:24666251-24667917	H1-neurons	neurons:	n/a	n/a
21	HCFC1	chr6:24665333-24668321	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr6:24666353-24667619	MCF-7	breast:	n/a	n/a
23	TBP	chr6:24665992-24667950	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr6:24666292-24667562	GM12878	blood:	n/a	n/a
25	CTCF	chr6:24666340-24666490	NHLF	lung:	n/a	n/a
26	POLR2A	chr6:24666108-24668118	H1-hESC	embryonic stem cell:	n/a	n/a
27	TBL1XR1	chr6:24666327-24667671	GM12878	blood:	n/a	n/a
28	WRNIP1	chr6:24666198-24667710	GM12878	blood:	n/a	n/a
29	RFX5	chr6:24666080-24668040	Hela-S3	cervix:	n/a	n/a
30	GATA1	chr6:24666196-24668062	PBDE	blood:	n/a	chr6:24667610-24667620
31	MBD4	chr6:24666338-24667881	HepG2	liver:	n/a	n/a
32	RELA	chr6:24666351-24667914	GM18505	blood:	n/a	n/a
33	POLR2A	chr6:24666353-24667563	H1-neurons	neurons:	n/a	n/a
34	BRCA1	chr6:24666298-24667732	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr6:24666324-24668021	GM12891	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24645863..24648986-chr6:24665821..24668897,5	MCF-7	breast:
2	chr6:24665480..24670247-chr6:24773496..24779775,9	K562	blood:
3	chr6:24666041..24667769-chr6:24719597..24721263,2	MCF-7	breast:
4	chr6:24494650..24496587-chr6:24665440..24668079,2	MCF-7	breast:
5	chr6:24494081..24496615-chr6:24665704..24668263,2	K562	blood:
6	chr6:24660920..24672880-chr6:24713381..24723000,42	K562	blood:
7	chr6:24665745..24668755-chr6:24718443..24722281,4	MCF-7	breast:
8	chr6:24661385..24670379-chr6:24713871..24722680,32	K562	blood:
9	chr6:24645218..24647641-chr6:24665331..24668427,5	MCF-7	breast:

No data

Variant related genes	Relation type
ACOT13	TF binding region
ENSG00000112293	Chromatin interaction
ENSG00000112312	Chromatin interaction
ENSG00000112308	Chromatin interaction
ENSG00000112294	Chromatin interaction
ENSG00000137261	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10085192	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12393	0.82[ASN][1000 genomes]
rs16889581	1.00[ASN][1000 genomes]
rs17243493	1.00[EUR][1000 genomes]
rs17243499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17243513	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249952	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6907640	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911150	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920675	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295629	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461051	0.87[ASN][1000 genomes]
rs9467250	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467261	0.87[ASN][1000 genomes]
rs9467263	0.87[ASN][1000 genomes]
rs9467265	0.87[ASN][1000 genomes]
rs9467267	0.87[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	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 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	chr6:24647000-24666400	Weak transcription	Esophagus	oesophagus
2	chr6:24662600-24666400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:24664000-24666400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:24664000-24668600	Active TSS	Colonic Mucosa	Colon
5	chr6:24664400-24668000	Active TSS	Fetal Intestine Large	intestine
6	chr6:24664600-24668000	Active TSS	Fetal Intestine Small	intestine
7	chr6:24664800-24666800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr6:24665000-24666400	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr6:24665000-24666400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr6:24665000-24666600	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr6:24665000-24666800	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr6:24665200-24666400	Flanking Active TSS	Brain Angular Gyrus	brain
13	chr6:24665200-24666400	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr6:24665200-24666600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:24665400-24666400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:24665400-24666400	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr6:24665400-24666400	Flanking Active TSS	Brain Substantia Nigra	brain
18	chr6:24665400-24666400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr6:24665400-24666600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:24665400-24666800	Flanking Active TSS	Liver	Liver
21	chr6:24665400-24667000	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr6:24665400-24668000	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr6:24665400-24668200	Active TSS	Psoas Muscle	Psoas
24	chr6:24665400-24668200	Active TSS	NHDF-Ad	bronchial
25	chr6:24665600-24666400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:24665600-24666400	Weak transcription	Spleen	Spleen
27	chr6:24665600-24666400	Flanking Active TSS	Dnd41	blood
28	chr6:24665600-24666400	Flanking Active TSS	Osteobl	bone
29	chr6:24665600-24666600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:24665600-24666600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:24665600-24666600	Flanking Active TSS	Fetal Lung	lung
32	chr6:24665600-24666800	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr6:24665600-24667800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:24665600-24668000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr6:24665600-24668000	Active TSS	GM12878-XiMat	blood
36	chr6:24665600-24668200	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr6:24665600-24668200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:24665600-24668200	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr6:24665600-24668400	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr6:24665600-24668400	Active TSS	NHLF	lung
41	chr6:24665800-24666400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr6:24665800-24666400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr6:24665800-24666400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr6:24665800-24666400	Flanking Active TSS	Fetal Thymus	thymus
45	chr6:24665800-24666400	Active TSS	Right Atrium	heart
46	chr6:24665800-24666400	Flanking Active TSS	HMEC	breast
47	chr6:24665800-24666400	Flanking Active TSS	HUVEC	blood vessel
48	chr6:24665800-24666400	Flanking Active TSS	NH-A	brain
49	chr6:24665800-24666600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:24665800-24666600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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