Variant report

Variant	rs41273248
Chromosome Location	chr6:31554400-31554401
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	FOXM1	chr6:31554150-31554661	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:31554205-31554953	GM12892	blood:	n/a	n/a
3	MAX	chr6:31554382-31554847	K562	blood:	n/a	chr6:31554707-31554717
4	SPI1	chr6:31553703-31555296	HL-60	blood:	n/a	chr6:31553939-31553946 chr6:31554434-31554447 chr6:31554100-31554113 chr6:31553936-31553949
5	SPI1	chr6:31553678-31554736	HL-60	blood:	n/a	chr6:31553939-31553946 chr6:31554434-31554447 chr6:31554100-31554113 chr6:31553936-31553949
6	POLR2A	chr6:31554331-31554847	GM12878	blood:	n/a	n/a
7	SPI1	chr6:31554205-31554615	GM12891	blood:	n/a	chr6:31554434-31554447
8	POLR2A	chr6:31553880-31554706	NB4	blood:	n/a	n/a
9	POLR2A	chr6:31554204-31554652	SK-N-MC	brain:	n/a	n/a
10	RUNX3	chr6:31553234-31555132	GM12878	blood:	n/a	n/a
11	GABPA	chr6:31554148-31554944	HL-60	blood:	n/a	n/a
12	MAZ	chr6:31554228-31554686	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:31553276-31555303	GM12891	blood:	n/a	n/a
14	SPI1	chr6:31554291-31554497	GM12878	blood:	n/a	chr6:31554434-31554447
15	EBF1	chr6:31554255-31554985	GM12878	blood:	n/a	n/a
16	MAX	chr6:31553394-31554905	NB4	blood:	n/a	chr6:31554707-31554717
17	RELA	chr6:31554393-31555209	GM18951	blood:	n/a	n/a
18	POLR2A	chr6:31554318-31554859	GM18505	blood:	n/a	n/a
19	NFIC	chr6:31554175-31554593	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:31554350-31554438	GM12878	blood:	n/a	n/a
21	ZBTB7A	chr6:31554357-31554663	K562	blood:	n/a	chr6:31554529-31554537 chr6:31554530-31554538
22	TAF1	chr6:31554299-31554669	GM12878	blood:	n/a	n/a
23	MYC	chr6:31553348-31555039	NB4	blood:	n/a	chr6:31554707-31554717
24	SPI1	chr6:31553945-31554933	GM12878	blood:	n/a	chr6:31554434-31554447 chr6:31554100-31554113
25	POLR2A	chr6:31554285-31554766	GM12892	blood:	n/a	n/a
26	SPI1	chr6:31554329-31554499	K562	blood:	n/a	chr6:31554434-31554447
27	PML	chr6:31553332-31555110	GM12878	blood:	n/a	n/a
28	RUNX3	chr6:31553837-31555240	GM12878	blood:	n/a	n/a
29	POLR2A	chr6:31554346-31554729	GM12891	blood:	n/a	n/a
30	SPI1	chr6:31554179-31554652	GM12891	blood:	n/a	chr6:31554434-31554447
31	MTA3	chr6:31553279-31555452	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:31554378-31554815	GM15510	blood:	n/a	n/a
33	POLR2A	chr6:31554320-31554764	GM12892	blood:	n/a	n/a
34	YY1	chr6:31554225-31554661	GM12892	blood:	n/a	chr6:31554293-31554304
35	YY1	chr6:31554400-31554685	GM12891	blood:	n/a	n/a
36	SPI1	chr6:31554244-31554551	K562	blood:	n/a	chr6:31554434-31554447
37	POLR2A	chr6:31554398-31554653	Raji	blood:	n/a	n/a
38	POLR2A	chr6:31554118-31554984	GM12892	blood:	n/a	n/a
39	YY1	chr6:31554345-31554733	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:31554370-31554748	GM12878	blood:	n/a	n/a
41	ELF1	chr6:31554265-31554832	GM12878	blood:	n/a	n/a
42	SPI1	chr6:31554200-31554612	GM12878	blood:	n/a	chr6:31554434-31554447
43	POLR2A	chr6:31554229-31554829	GM12891	blood:	n/a	n/a
44	POLR2A	chr6:31554257-31554983	GM12892	blood:	n/a	n/a
45	REST	chr6:31553322-31554995	HL-60	blood:	n/a	chr6:31554667-31554681 chr6:31554560-31554573
46	POLR2A	chr6:31553219-31556579	HL-60	blood:	n/a	n/a
47	POLR2A	chr6:31554326-31554821	GM12878	blood:	n/a	n/a
48	POLR2A	chr6:31554324-31554842	GM19193	blood:	n/a	n/a
49	POLR2A	chr6:31554246-31554812	GM12891	blood:	n/a	n/a
50	BCLAF1	chr6:31554189-31554708	GM12878	blood:	n/a	chr6:31554545-31554558

No.	Distal block	Cell Line	Cell type
1	chr6:31552844..31558545-chr6:31585940..31590373,6	MCF-7	breast:
2	chr6:31504163..31505807-chr6:31553769..31555634,2	K562	blood:
3	chr6:31553317..31555989-chr6:31586068..31588677,3	K562	blood:
4	chr6:31553044..31555571-chr6:31558809..31560803,3	K562	blood:
5	chr6:31514907..31516609-chr6:31553664..31555666,2	MCF-7	breast:

Variant related genes	Relation type
LTB	TF binding region
LST1	TF binding region
ENSG00000201785	Chromatin interaction
ENSG00000213760	Chromatin interaction
ENSG00000204475	Chromatin interaction
ENSG00000204498	Chromatin interaction
ENSG00000204469	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs17201192	1.00[ASN][1000 genomes]
rs35595439	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55786861	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55799418	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932544	1.00[ASN][1000 genomes]
rs56061694	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56127727	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56229298	1.00[ASN][1000 genomes]
rs61740977	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs915653	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9469058	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
2	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
3	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
4	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
5	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
6	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
7	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
8	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
9	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
10	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
11	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
12	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
13	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
14	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
15	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31549400-31555600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:31549400-31556200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr6:31550000-31555000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:31550000-31556200	Weak transcription	Gastric	stomach
5	chr6:31550000-31583200	Weak transcription	Right Atrium	heart
6	chr6:31550200-31555200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:31550200-31556800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:31550400-31554600	Weak transcription	Brain Hippocampus Middle	brain
9	chr6:31550800-31560400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:31552400-31555400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr6:31552600-31555200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr6:31552600-31557200	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr6:31552800-31555200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:31552800-31556000	Enhancers	Dnd41	blood
15	chr6:31553000-31555400	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr6:31553000-31556400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr6:31553200-31554800	Bivalent Enhancer	Placenta	Placenta
18	chr6:31553200-31555200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:31553200-31555200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr6:31553200-31556600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr6:31553400-31554800	Enhancers	Spleen	Spleen
22	chr6:31553400-31556600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:31553400-31557000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr6:31553400-31557400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:31553400-31557600	Enhancers	K562	blood
26	chr6:31553600-31554600	Bivalent Enhancer	Adipose Nuclei	Adipose
27	chr6:31553600-31555800	Flanking Active TSS	Thymus	Thymus
28	chr6:31553600-31556600	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr6:31553600-31556600	Flanking Active TSS	Fetal Thymus	thymus
30	chr6:31553600-31557000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:31553800-31554400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:31553800-31554800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:31553800-31554800	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr6:31553800-31555200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr6:31553800-31555600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr6:31553800-31556200	Active TSS	Duodenum Mucosa	Duodenum
37	chr6:31553800-31556400	Weak transcription	Liver	Liver
38	chr6:31554000-31554800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr6:31554000-31554800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr6:31554000-31554800	Enhancers	Esophagus	oesophagus
41	chr6:31554000-31554800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr6:31554000-31555000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr6:31554000-31556600	Flanking Active TSS	GM12878-XiMat	blood
44	chr6:31554200-31554400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
45	chr6:31554200-31554600	Enhancers	Primary B cells from peripheral blood	blood
46	chr6:31554200-31554600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr6:31554200-31554600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:31554200-31554800	Flanking Active TSS	Colonic Mucosa	Colon
49	chr6:31554200-31555000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr6:31554200-31556400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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