Variant report

Variant	rs71564870
Chromosome Location	chr6:56818846-56818847
allele	C/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	CCNT2	chr6:56818752-56820369	K562	blood:	n/a	n/a
2	MYC	chr6:56818414-56821029	K562	blood:	n/a	chr6:56819810-56819817 chr6:56819809-56819818 chr6:56818787-56818795 chr6:56819807-56819822 chr6:56819596-56819605 chr6:56820510-56820519 chr6:56818675-56818684 chr6:56819809-56819819
3	POLR2A	chr6:56818401-56820972	GM18505	blood:	n/a	n/a
4	POLR2A	chr6:56818599-56820925	IMR90	lung:	n/a	n/a
5	POLR2A	chr6:56818258-56821041	GM19099	blood:	n/a	n/a
6	TBP	chr6:56818844-56821002	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr6:56818566-56821126	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:56817860-56821003	GM12878	blood:	n/a	n/a
9	IKZF1	chr6:56818271-56818865	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:56818137-56819678	GM12878	blood:	n/a	n/a
11	MAX	chr6:56818543-56818948	GM12878	blood:	n/a	chr6:56818787-56818795 chr6:56818675-56818684
12	ATF2	chr6:56818259-56818890	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:56818805-56820457	MCF-7	breast:	n/a	n/a
14	TEAD4	chr6:56818508-56819052	K562	blood:	n/a	n/a
15	YY1	chr6:56818570-56818970	GM12878	blood:	n/a	n/a
16	MAZ	chr6:56818322-56819228	GM12878	blood:	n/a	chr6:56818787-56818795 chr6:56818675-56818684
17	FOXM1	chr6:56818276-56818920	GM12878	blood:	n/a	n/a
18	BATF	chr6:56818274-56819000	GM12878	blood:	n/a	chr6:56818675-56818686
19	MAX	chr6:56818182-56821026	NB4	blood:	n/a	chr6:56819810-56819817 chr6:56819809-56819818 chr6:56818787-56818795 chr6:56819807-56819822 chr6:56819596-56819605 chr6:56820510-56820519 chr6:56818675-56818684 chr6:56819809-56819819
20	HA-E2F1	chr6:56818534-56821134	MCF-7	breast:	n/a	chr6:56819846-56819856 chr6:56819865-56819877 chr6:56819009-56819018
21	TCF7L2	chr6:56818837-56819486	Hela-S3	cervix:	n/a	n/a
22	RUNX3	chr6:56818299-56819583	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:56818571-56821038	GM19193	blood:	n/a	n/a
24	NFIC	chr6:56818104-56818905	GM12878	blood:	n/a	n/a
25	RELA	chr6:56818308-56820949	GM15510	blood:	n/a	chr6:56820275-56820284 chr6:56820275-56820284
26	POLR2A	chr6:56818488-56819056	GM12891	blood:	n/a	n/a
27	ZNF263	chr6:56818346-56820896	HEK293-T-REx	kidney:	n/a	chr6:56818755-56818764
28	POLR2A	chr6:56818155-56821044	GM12891	blood:	n/a	n/a
29	MTA3	chr6:56818140-56819528	GM12878	blood:	n/a	n/a
30	EP300	chr6:56818724-56821068	SK-N-SH	brain:	n/a	chr6:56819773-56819782 chr6:56819997-56820013 chr6:56819855-56819871 chr6:56819596-56819605 chr6:56819925-56819941 chr6:56819962-56819978 chr6:56819776-56819785 chr6:56820620-56820634 chr6:56820615-56820628
31	POLR2A	chr6:56818489-56818854	GM12891	blood:	n/a	n/a
32	RUNX3	chr6:56818195-56819032	GM12878	blood:	n/a	n/a
33	MAZ	chr6:56818157-56821098	IMR90	lung:	n/a	chr6:56819810-56819817 chr6:56819809-56819818 chr6:56818787-56818795 chr6:56819807-56819822 chr6:56819596-56819605 chr6:56820510-56820519 chr6:56818675-56818684 chr6:56819809-56819819
34	WRNIP1	chr6:56818192-56818907	GM12878	blood:	n/a	n/a
35	MYC	chr6:56818484-56821014	K562	blood:	n/a	chr6:56819810-56819817 chr6:56819809-56819818 chr6:56818787-56818795 chr6:56819807-56819822 chr6:56819596-56819605 chr6:56820510-56820519 chr6:56818675-56818684 chr6:56819809-56819819
36	MAZ	chr6:56818515-56821074	K562	blood:	n/a	chr6:56819810-56819817 chr6:56819809-56819818 chr6:56818787-56818795 chr6:56819807-56819822 chr6:56819596-56819605 chr6:56820510-56820519 chr6:56818675-56818684 chr6:56819809-56819819
37	CTBP2	chr6:56818607-56820454	H1-hESC	embryonic stem cell:	n/a	n/a
38	MXI1	chr6:56817851-56821832	SK-N-SH	brain:	n/a	chr6:56820811-56820820 chr6:56819810-56819819
39	POLR2A	chr6:56818323-56821034	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:56818572-56820401	GM12878	blood:	n/a	n/a
41	STAT5A	chr6:56818466-56819107	GM12878	blood:	n/a	chr6:56818674-56818683 chr6:56818751-56818763 chr6:56818979-56818991
42	POLR2A	chr6:56818231-56821022	GM12891	blood:	n/a	n/a
43	POLR2A	chr6:56818531-56820999	GM15510	blood:	n/a	n/a
44	RELA	chr6:56818225-56819590	GM19193	blood:	n/a	n/a
45	SMARCB1	chr6:56818651-56820956	Hela-S3	cervix:	n/a	n/a
46	MXI1	chr6:56817775-56821104	IMR90	lung:	n/a	chr6:56820811-56820820 chr6:56819810-56819819
47	BACH1	chr6:56818233-56820972	H1-hESC	embryonic stem cell:	n/a	chr6:56819593-56819607 chr6:56818672-56818686
48	POLR2A	chr6:56818659-56820983	Hela-S3	cervix:	n/a	n/a
49	JUND	chr6:56818519-56819623	H1-hESC	embryonic stem cell:	n/a	chr6:56819596-56819603 chr6:56818674-56818683 chr6:56819596-56819604 chr6:56819596-56819604 chr6:56818673-56818684 chr6:56819595-56819605 chr6:56819594-56819606
50	POLR2A	chr6:56818317-56819699	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:56818167..56820292-chr6:57177596..57182762,4	MCF-7	breast:
2	chr6:56818015..56821855-chr6:57180367..57183028,4	K562	blood:
3	chr6:56817930..56821539-chr6:56909452..56912838,6	K562	blood:
4	chr6:56809927..56811973-chr6:56817461..56820564,4	MCF-7	breast:
5	chr6:56816669..56821714-chr6:56908406..56912975,10	K562	blood:
6	chr6:56817813..56820711-chr6:56965881..56967844,2	K562	blood:
7	chr6:56818718..56821144-chr6:56954189..56956169,2	MCF-7	breast:
8	chr6:56818586..56820160-chr6:56954804..56956394,2	K562	blood:
9	chr6:56817242..56820030-chr9:96215701..96218251,2	MCF-7	breast:
10	chr6:56817510..56820425-chr6:57182215..57184592,2	K562	blood:
11	chr6:56817882..56819972-chr6:57035811..57037517,2	K562	blood:
12	chr6:56818533..56822842-chr6:56954657..56959004,6	K562	blood:
13	chr6:56818562..56821573-chr6:56964600..56969072,4	K562	blood:
14	chr6:56714424..56718313-chr6:56818301..56821248,4	MCF-7	breast:

Variant related genes	Relation type
BEND6	TF binding region
ENSG00000226803	Chromatin interaction
ENSG00000146143	Chromatin interaction
ENSG00000168116	Chromatin interaction
ENSG00000112208	Chromatin interaction
ENSG00000188938	Chromatin interaction
ENSG00000200224	Chromatin interaction
ENSG00000151914	Chromatin interaction
ENSG00000112200	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1020548	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13193465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13193800	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13198484	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13207800	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13212013	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13214032	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13214255	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13218276	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13220575	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1451707	0.83[AMR][1000 genomes]
rs1451708	0.83[AMR][1000 genomes]
rs17685277	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17685338	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17685380	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2613119	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2817573	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28360535	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28360536	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28360537	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28360538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34009699	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34027274	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34399458	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34616943	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34812189	0.86[AMR][1000 genomes]
rs34979183	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35090265	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35336675	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35434542	0.83[AMR][1000 genomes]
rs35605425	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35735810	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35899012	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35961728	0.83[AMR][1000 genomes]
rs36124814	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55952713	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56381984	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6901944	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6904924	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6906623	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6907143	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6927558	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71564869	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71564872	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs720884	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7760385	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats 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 miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv3514081	chr6:56818693-56821116	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
9	esv3514082	chr6:56818693-56821116	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs71564870	BEND6	cis	Esophagus Mucosa	GTEx
rs71564870	BEND6	cis	Thyroid	GTEx
rs71564870	BEND6	cis	Esophagus Muscularis	GTEx
rs71564870	BEND6	cis	Muscle Skeletal	GTEx
rs71564870	BEND6	cis	Artery Tibial	GTEx
rs71564870	BEND6	cis	Heart Left Ventricle	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56817000-56820600	Active TSS	NHLF	lung
2	chr6:56817400-56819000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:56817800-56819200	Flanking Active TSS	Hela-S3	cervix
4	chr6:56817800-56819400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:56817800-56821200	Active TSS	NHDF-Ad	bronchial
6	chr6:56818000-56820400	Active TSS	Muscle Satellite Cultured Cells	--
7	chr6:56818000-56820600	Active TSS	Colon Smooth Muscle	Colon
8	chr6:56818000-56821000	Active TSS	HSMM	muscle
9	chr6:56818000-56821200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:56818000-56821400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr6:56818200-56819000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:56818200-56819000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:56818200-56819000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:56818200-56819000	Enhancers	Spleen	Spleen
15	chr6:56818200-56819200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr6:56818200-56819200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
17	chr6:56818200-56819400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
18	chr6:56818200-56819400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr6:56818200-56819400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:56818200-56819400	Flanking Active TSS	Placenta	Placenta
21	chr6:56818200-56819400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
22	chr6:56818200-56819400	Active TSS	Right Atrium	heart
23	chr6:56818200-56819400	Flanking Active TSS	HUVEC	blood vessel
24	chr6:56818200-56820200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:56818200-56820200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
26	chr6:56818200-56820400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:56818200-56820400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:56818200-56820800	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr6:56818200-56820800	Active TSS	Aorta	Aorta
30	chr6:56818200-56821000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:56818200-56821000	Bivalent/Poised TSS	Fetal Kidney	kidney
32	chr6:56818200-56821000	Active TSS	Rectal Smooth Muscle	rectum
33	chr6:56818200-56821000	Active TSS	A549	lung
34	chr6:56818400-56819000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:56818400-56819000	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
36	chr6:56818400-56819200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
37	chr6:56818400-56819200	Bivalent Enhancer	Fetal Heart	heart
38	chr6:56818400-56819200	Flanking Bivalent TSS/Enh	Fetal Lung	lung
39	chr6:56818400-56819200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
40	chr6:56818400-56819400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
41	chr6:56818400-56819400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
42	chr6:56818400-56819400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
43	chr6:56818400-56819400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
44	chr6:56818400-56819400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
45	chr6:56818400-56819400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
46	chr6:56818400-56819400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
47	chr6:56818400-56819400	Flanking Bivalent TSS/Enh	Liver	Liver
48	chr6:56818400-56819400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
49	chr6:56818400-56819400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
50	chr6:56818400-56819600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood

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