Variant report

Variant	rs41288576
Chromosome Location	chr6:110501222-110501223
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	MAX	chr6:110499784-110501606	ECC-1	luminal epithelium:	n/a	chr6:110500883-110500893
2	STAT3	chr6:110501196-110501515	MCF10A-Er-Src	breast:	n/a	n/a
3	TBL1XR1	chr6:110500734-110501363	K562	blood:	n/a	n/a
4	CEBPB	chr6:110500926-110501387	ECC-1	luminal epithelium:	n/a	chr6:110501161-110501172 chr6:110501159-110501170
5	FOS	chr6:110501120-110501509	MCF10A-Er-Src	breast:	n/a	n/a
6	TFAP2C	chr6:110499855-110501990	Hela-S3	cervix:	n/a	chr6:110501373-110501388
7	SP1	chr6:110501031-110501556	GM12878	blood:	n/a	chr6:110501259-110501268 chr6:110501258-110501268 chr6:110501257-110501268 chr6:110501093-110501105 chr6:110501180-110501189 chr6:110501258-110501268 chr6:110501287-110501298 chr6:110501257-110501269 chr6:110501176-110501190 chr6:110501287-110501299 chr6:110501277-110501287 chr6:110501258-110501267 chr6:110501257-110501269 chr6:110501259-110501268 chr6:110501100-110501110 chr6:110501277-110501287 chr6:110501287-110501299
8	POLR2A	chr6:110500563-110502149	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr6:110500667-110501291	U87	brain:	n/a	n/a
10	RCOR1	chr6:110500768-110501882	K562	blood:	n/a	n/a
11	GABPA	chr6:110501186-110501411	GM12878	blood:	n/a	chr6:110501258-110501267
12	EP300	chr6:110500645-110501798	HepG2	liver:	n/a	chr6:110501160-110501174 chr6:110500763-110500779 chr6:110501038-110501052 chr6:110501098-110501111
13	MAX	chr6:110501207-110501899	H1-hESC	embryonic stem cell:	n/a	n/a
14	YY1	chr6:110500548-110501531	HepG2	liver:	n/a	chr6:110500803-110500817 chr6:110501258-110501267 chr6:110500882-110500891
15	POLR2A	chr6:110500609-110501966	GM18951	blood:	n/a	n/a
16	POLR2A	chr6:110500603-110502018	IMR90	lung:	n/a	n/a
17	POLR2A	chr6:110500616-110501968	GM18505	blood:	n/a	n/a
18	YY1	chr6:110500828-110502106	SK-N-SH	brain:	n/a	chr6:110501258-110501267 chr6:110500882-110500891
19	PML	chr6:110500961-110501829	K562	blood:	n/a	n/a
20	EGR1	chr6:110500759-110501597	K562	blood:	n/a	chr6:110501097-110501108 chr6:110501280-110501289 chr6:110501095-110501110 chr6:110501307-110501331 chr6:110500884-110500894 chr6:110500881-110500891 chr6:110501279-110501292 chr6:110501290-110501303 chr6:110500882-110500897 chr6:110501290-110501303 chr6:110501289-110501304 chr6:110501096-110501109 chr6:110500883-110500896 chr6:110501253-110501266 chr6:110500883-110500896
21	MYC	chr6:110500600-110501893	K562	blood:	n/a	chr6:110500883-110500893
22	YY1	chr6:110500967-110501879	GM12892	blood:	n/a	chr6:110501258-110501267
23	E2F4	chr6:110500653-110501605	MCF10A-Er-Src	breast:	n/a	chr6:110500882-110500891 chr6:110500820-110500830 chr6:110501258-110501267
24	ZBTB33	chr6:110501125-110501437	GM12878	blood:	n/a	chr6:110501327-110501342
25	POLR2A	chr6:110500559-110501839	HCT-116	colon:	n/a	n/a
26	BCLAF1	chr6:110501051-110501992	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:110499728-110502029	H1-neurons	neurons:	n/a	n/a
28	ZBTB7A	chr6:110499747-110501447	ECC-1	luminal epithelium:	n/a	chr6:110500461-110500472
29	MYC	chr6:110501190-110501409	MCF-7	breast:	n/a	n/a
30	SIN3A	chr6:110499745-110502166	H1-hESC	embryonic stem cell:	n/a	chr6:110501583-110501597 chr6:110500453-110500464
31	ATF2	chr6:110500953-110501814	GM12878	blood:	n/a	n/a
32	NFIC	chr6:110500883-110501410	HepG2	liver:	n/a	n/a
33	POLR2A	chr6:110500574-110501360	ECC-1	luminal epithelium:	n/a	n/a
34	CEBPB	chr6:110500742-110501840	HepG2	liver:	n/a	chr6:110501161-110501172 chr6:110501159-110501170
35	POLR2A	chr6:110499888-110502205	Hela-S3	cervix:	n/a	n/a
36	SPI1	chr6:110501136-110501408	GM12891	blood:	n/a	n/a
37	POLR2A	chr6:110499761-110501899	PANC-1	pancreas:	n/a	n/a
38	GABPA	chr6:110500884-110502100	SK-N-SH	brain:	n/a	chr6:110501258-110501267
39	MAX	chr6:110500543-110501905	ECC-1	luminal epithelium:	n/a	chr6:110500883-110500893
40	USF2	chr6:110501097-110501782	GM12878	blood:	n/a	n/a
41	JUND	chr6:110500811-110501234	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr6:110500515-110501967	U87	brain:	n/a	n/a
43	ETS1	chr6:110501063-110501576	GM12878	blood:	n/a	chr6:110501307-110501320 chr6:110501332-110501343 chr6:110501331-110501344 chr6:110501329-110501343
44	BRCA1	chr6:110501163-110501675	HepG2	liver:	n/a	n/a
45	FOXM1	chr6:110500833-110501721	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:110499620-110502082	SK-N-MC	brain:	n/a	n/a
47	YY1	chr6:110501118-110501859	GM12878	blood:	n/a	chr6:110501258-110501267
48	MAX	chr6:110500615-110501810	SK-N-SH	brain:	n/a	chr6:110500883-110500893
49	RFX5	chr6:110501148-110501776	GM12878	blood:	n/a	n/a
50	CEBPB	chr6:110500794-110501847	IMR90	lung:	n/a	chr6:110501161-110501172 chr6:110501159-110501170

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:110499653..110501302-chr6:110501539..110503482,2	MCF-7	breast:

Variant related genes	Relation type
WASF1	TF binding region
CDC40	TF binding region
ENSG00000168438	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12660108	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12662027	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12662099	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12662559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664024	0.87[EUR][1000 genomes]
rs12664697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665152	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665178	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665650	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1350943	0.87[EUR][1000 genomes]
rs1350944	0.87[EUR][1000 genomes]
rs1381688	0.87[EUR][1000 genomes]
rs2002631	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2361500	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2885293	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3806158	0.85[ASN][1000 genomes]
rs3828928	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41288574	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57771959	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58100980	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58965432	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59181827	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60105161	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61494781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904509	0.86[ASN][1000 genomes]
rs6918158	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922245	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6922536	0.87[EUR][1000 genomes]
rs6926993	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6927464	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935544	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6937364	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6940347	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6941101	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73765657	0.87[EUR][1000 genomes]
rs73765660	0.87[EUR][1000 genomes]
rs73765665	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7752069	0.87[EUR][1000 genomes]
rs7770634	0.87[EUR][1000 genomes]
rs7771649	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7771909	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9374151	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9374153	0.87[EUR][1000 genomes]
rs9374154	0.87[EUR][1000 genomes]
rs9374155	0.87[EUR][1000 genomes]
rs9374157	0.87[EUR][1000 genomes]
rs9386877	0.87[EUR][1000 genomes]
rs9386879	0.87[EUR][1000 genomes]
rs9400361	0.87[EUR][1000 genomes]
rs9487320	0.82[ASN][1000 genomes]
rs9487324	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886535	chr6:110377006-110551463	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	esv2757188	chr6:110389926-110504680	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	esv2759462	chr6:110389926-110504680	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv1792799	chr6:110411065-110566597	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv886536	chr6:110426046-110502831	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv948824	chr6:110443685-110889332	Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110498000-110502200	Active TSS	Brain Angular Gyrus	brain
2	chr6:110498600-110502200	Active TSS	Brain Anterior Caudate	brain
3	chr6:110498600-110502400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:110498800-110502200	Active TSS	Brain Cingulate Gyrus	brain
5	chr6:110498800-110502200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:110498800-110502200	Active TSS	HMEC	breast
7	chr6:110498800-110502400	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr6:110498800-110502400	Active TSS	Fetal Stomach	stomach
9	chr6:110499000-110501400	Active TSS	Fetal Brain Male	brain
10	chr6:110499000-110502200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:110499000-110502200	Active TSS	Fetal Brain Female	brain
12	chr6:110499200-110502400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:110499200-110502400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:110499200-110502400	Active TSS	Stomach Smooth Muscle	stomach
15	chr6:110499400-110502200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:110499400-110502200	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr6:110499400-110502200	Active TSS	NH-A	brain
18	chr6:110499400-110502400	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr6:110499400-110502400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:110499400-110502600	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr6:110499400-110502800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:110499400-110502800	Active TSS	A549	lung
23	chr6:110499400-110503000	Active TSS	H1 Cell Line	embryonic stem cell
24	chr6:110499400-110503000	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr6:110499400-110503200	Active TSS	K562	blood
26	chr6:110499600-110502000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:110499600-110502200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:110499600-110502200	Active TSS	Primary B cells from peripheral blood	blood
29	chr6:110499600-110502200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:110499600-110502200	Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr6:110499600-110502400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:110499600-110502400	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr6:110499600-110502400	Active TSS	Fetal Intestine Small	intestine
34	chr6:110499600-110502400	Active TSS	Thymus	Thymus
35	chr6:110499600-110502400	Active TSS	HSMM	muscle
36	chr6:110499600-110502600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:110499600-110502600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:110499600-110502600	Active TSS	HSMMtube	muscle
39	chr6:110499600-110502600	Active TSS	NHDF-Ad	bronchial
40	chr6:110499600-110502800	Active TSS	H9 Cell Line	embryonic stem cell
41	chr6:110499600-110502800	Active TSS	Fetal Kidney	kidney
42	chr6:110499600-110502800	Active TSS	GM12878-XiMat	blood
43	chr6:110499600-110503000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:110499600-110503000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:110499600-110503800	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr6:110499800-110502000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:110499800-110502000	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr6:110499800-110502200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr6:110499800-110502200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:110499800-110502200	Active TSS	Primary T helper cells PMA-I stimulated	--

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