Variant report

Variant	rs13193465
Chromosome Location	chr6:56820248-56820249
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	MXI1	chr6:56819263-56820856	Hela-S3	cervix:	n/a	chr6:56820811-56820820 chr6:56819810-56819819
2	FOXM1	chr6:56819976-56821002	GM12878	blood:	n/a	n/a
3	CCNT2	chr6:56818752-56820369	K562	blood:	n/a	n/a
4	NFIC	chr6:56819321-56821030	SK-N-SH	brain:	n/a	n/a
5	RELA	chr6:56819859-56821056	GM12891	blood:	n/a	chr6:56820275-56820284 chr6:56820275-56820284
6	CTCF	chr6:56820120-56820270	GM06990	blood:	n/a	n/a
7	TCF12	chr6:56819960-56820333	GM12878	blood:	n/a	n/a
8	CTCF	chr6:56819925-56820354	HepG2	liver:	n/a	chr6:56819999-56820012
9	MAX	chr6:56818922-56820994	K562	blood:	n/a	chr6:56819810-56819817 chr6:56819809-56819818 chr6:56819807-56819822 chr6:56819596-56819605 chr6:56820510-56820519 chr6:56819809-56819819
10	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
11	CTCF	chr6:56819885-56820252	SK-N-SH_RA	brain:	n/a	chr6:56819999-56820012
12	CTCF	chr6:56819992-56820248	LNCaP	prostate:	n/a	chr6:56819999-56820012
13	SP1	chr6:56819985-56820336	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:56819848-56820916	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:56818401-56820972	GM18505	blood:	n/a	n/a
16	E2F6	chr6:56819229-56820334	K562	blood:	n/a	chr6:56819846-56819856 chr6:56819865-56819877
17	ELF1	chr6:56819870-56820409	SK-N-SH	brain:	n/a	chr6:56819882-56819894
18	CTCF	chr6:56819954-56820273	GM12891	blood:	n/a	chr6:56819999-56820012
19	POLR2A	chr6:56819228-56820510	ECC-1	luminal epithelium:	n/a	n/a
20	WRNIP1	chr6:56820156-56820944	GM12878	blood:	n/a	n/a
21	TCF12	chr6:56819811-56820954	ECC-1	luminal epithelium:	n/a	n/a
22	MYC	chr6:56819915-56820324	H1-hESC	embryonic stem cell:	n/a	n/a
23	CREB1	chr6:56819279-56820347	H1-hESC	embryonic stem cell:	n/a	chr6:56819901-56819914
24	RAD21	chr6:56819912-56820306	A549	lung:	n/a	n/a
25	MAX	chr6:56819179-56820477	H1-hESC	embryonic stem cell:	n/a	chr6:56819810-56819817 chr6:56819809-56819818 chr6:56819807-56819822 chr6:56819596-56819605 chr6:56819809-56819819
26	POLR2A	chr6:56818599-56820925	IMR90	lung:	n/a	n/a
27	RFX5	chr6:56819842-56820500	Hela-S3	cervix:	n/a	n/a
28	E2F4	chr6:56819300-56820969	K562	blood:	n/a	chr6:56819846-56819856 chr6:56819865-56819877
29	POLR2A	chr6:56818258-56821041	GM19099	blood:	n/a	n/a
30	TBP	chr6:56818844-56821002	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr6:56819026-56820948	K562	blood:	n/a	n/a
32	YY1	chr6:56819210-56821039	SK-N-SH	brain:	n/a	chr6:56819546-56819557 chr6:56819962-56819976 chr6:56819543-56819557 chr6:56819534-56819548 chr6:56819775-56819784 chr6:56819846-56819860 chr6:56819922-56819933 chr6:56819514-56819528 chr6:56819770-56819784
33	SIN3AK20	chr6:56819350-56820393	K562	blood:	n/a	n/a
34	ZMIZ1	chr6:56820030-56820495	K562	blood:	n/a	n/a
35	CREB1	chr6:56820026-56820269	A549	lung:	n/a	n/a
36	CTCF	chr6:56819868-56821047	K562	blood:	n/a	chr6:56820848-56820864 chr6:56819999-56820012
37	POLR2A	chr6:56819096-56820950	HepG2	liver:	n/a	n/a
38	E2F4	chr6:56819891-56820313	MCF10A-Er-Src	breast:	n/a	n/a
39	ELK1	chr6:56819919-56820549	Hela-S3	cervix:	n/a	n/a
40	RAD21	chr6:56819903-56820422	MCF-7	breast:	n/a	n/a
41	JUND	chr6:56819914-56821016	H1-hESC	embryonic stem cell:	n/a	chr6:56820014-56820023 chr6:56820510-56820518 chr6:56820509-56820519
42	POLR2A	chr6:56819386-56820448	K562	blood:	n/a	n/a
43	SMC3	chr6:56819966-56820272	HepG2	liver:	n/a	n/a
44	RAD21	chr6:56819988-56820327	GM12878	blood:	n/a	n/a
45	POLR2A	chr6:56818566-56821126	H1-hESC	embryonic stem cell:	n/a	n/a
46	TCF12	chr6:56819975-56820357	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr6:56819909-56820259	Hela-S3	cervix:	n/a	chr6:56819999-56820012
48	POLR2A	chr6:56820149-56820442	GM12878	blood:	n/a	n/a
49	PAX5	chr6:56819664-56820331	GM12892	blood:	n/a	chr6:56819930-56819939 chr6:56820297-56820306 chr6:56819928-56819937
50	POLR2A	chr6:56817860-56821003	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:56716516..56717082-chr6:56820161..56820759,2	MCF-7	breast:
2	chr6:56818167..56820292-chr6:57177596..57182762,4	MCF-7	breast:
3	chr6:56818015..56821855-chr6:57180367..57183028,4	K562	blood:
4	chr6:56819605..56821184-chr6:57037443..57039145,2	K562	blood:
5	chr6:56817930..56821539-chr6:56909452..56912838,6	K562	blood:
6	chr6:56809927..56811973-chr6:56817461..56820564,4	MCF-7	breast:
7	chr6:56816669..56821714-chr6:56908406..56912975,10	K562	blood:
8	chr6:56817813..56820711-chr6:56965881..56967844,2	K562	blood:
9	chr6:56818718..56821144-chr6:56954189..56956169,2	MCF-7	breast:
10	chr6:56817510..56820425-chr6:57182215..57184592,2	K562	blood:
11	chr6:56818533..56822842-chr6:56954657..56959004,6	K562	blood:
12	chr6:56818562..56821573-chr6:56964600..56969072,4	K562	blood:
13	chr6:56714424..56718313-chr6:56818301..56821248,4	MCF-7	breast:

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

Extended variants
information (count: 70 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1007417	0.84[TSI][hapmap]
rs1020548	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1044670	0.83[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
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[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13220575	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];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]
rs1562908	0.84[TSI][hapmap]
rs1599280	1.00[GIH][hapmap]
rs17685277	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17685338	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17685380	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2397227	0.84[TSI][hapmap]
rs2613119	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2817573	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6904172	0.84[TSI][hapmap]
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]
rs71564870	1.00[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	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs720885	0.84[TSI][hapmap]
rs7760385	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9382669	0.84[TSI][hapmap]
rs9382670	0.84[TSI][hapmap]
rs9396246	0.84[TSI][hapmap]
rs9396250	0.84[TSI][hapmap]
rs9475758	0.84[TSI][hapmap]
rs9475760	0.84[TSI][hapmap]
rs9475763	0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	esv3437533	chr6:56819343-56820491	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs13193465	BEND6	cis	lymphoblastoid	seeQTL
rs13193465	BEND6	cis	Heart Left Ventricle	GTEx
rs13193465	BEND6	cis	Esophagus Muscularis	GTEx
rs13193465	BEND6	cis	Artery Tibial	GTEx
rs13193465	BEND6	cis	cerebellum	SCAN
rs13193465	BEND6	cis	Esophagus Mucosa	GTEx
rs13193465	BEND6	cis	Muscle Skeletal	GTEx
rs13193465	BEND6	cis	Thyroid	GTEx
rs13193465	C6orf65	cis	multi-tissue	Pritchard
rs13193465	DST	cis	cerebellum	SCAN
rs13193465	BEND6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56817000-56820600	Active TSS	NHLF	lung
2	chr6:56817800-56821200	Active TSS	NHDF-Ad	bronchial
3	chr6:56818000-56820400	Active TSS	Muscle Satellite Cultured Cells	--
4	chr6:56818000-56820600	Active TSS	Colon Smooth Muscle	Colon
5	chr6:56818000-56821000	Active TSS	HSMM	muscle
6	chr6:56818000-56821200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:56818000-56821400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr6:56818200-56820400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:56818200-56820400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:56818200-56820800	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr6:56818200-56820800	Active TSS	Aorta	Aorta
12	chr6:56818200-56821000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:56818200-56821000	Bivalent/Poised TSS	Fetal Kidney	kidney
14	chr6:56818200-56821000	Active TSS	Rectal Smooth Muscle	rectum
15	chr6:56818200-56821000	Active TSS	A549	lung
16	chr6:56818400-56820400	Active TSS	HSMMtube	muscle
17	chr6:56818400-56820600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:56818400-56820600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:56818400-56820600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:56818400-56820600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:56818400-56820800	Active TSS	Ovary	ovary
22	chr6:56818400-56820800	Active TSS	Psoas Muscle	Psoas
23	chr6:56818400-56821000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:56818400-56821000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:56818400-56821000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:56818400-56821000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:56818400-56821000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:56818400-56821000	Active TSS	GM12878-XiMat	blood
29	chr6:56818400-56821000	Active TSS	Osteobl	bone
30	chr6:56818400-56821200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:56818400-56821800	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr6:56818600-56820400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:56818600-56820600	Active TSS	NHEK	skin
34	chr6:56818600-56820800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr6:56818600-56820800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:56818600-56820800	Active TSS	Brain Hippocampus Middle	brain
37	chr6:56818600-56821200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
38	chr6:56818600-56821200	Active TSS	K562	blood
39	chr6:56818600-56821400	Active TSS	Brain Anterior Caudate	brain
40	chr6:56818600-56821800	Active TSS	Brain Angular Gyrus	brain
41	chr6:56818800-56820400	Active TSS	NH-A	brain
42	chr6:56818800-56820600	Active TSS	Brain Cingulate Gyrus	brain
43	chr6:56818800-56820600	Bivalent/Poised TSS	Small Intestine	intestine
44	chr6:56818800-56820800	Active TSS	Brain Substantia Nigra	brain
45	chr6:56818800-56821000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:56818800-56821000	Active TSS	H9 Cell Line	embryonic stem cell
47	chr6:56819000-56820400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:56819000-56821000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:56819000-56821200	Active TSS	Fetal Brain Female	brain
50	chr6:56819200-56820400	Active TSS	Sigmoid Colon	Sigmoid Colon

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