Variant report

Variant	rs6459178
Chromosome Location	chr6:56954518-56954519
allele	A/C
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	USF2	chr6:56954469-56954998	GM12878	blood:	n/a	chr6:56954714-56954730
2	POLR2A	chr6:56954436-56955204	HEK293	kidney:	n/a	n/a
3	STAT5A	chr6:56954465-56955072	GM12878	blood:	n/a	n/a
4	SP1	chr6:56954397-56955086	HCT-116	colon:	n/a	chr6:56954712-56954722 chr6:56954712-56954722 chr6:56954711-56954722 chr6:56954711-56954723
5	NFATC1	chr6:56954440-56955097	GM12878	blood:	n/a	n/a
6	SIN3AK20	chr6:56954499-56955118	H1-hESC	embryonic stem cell:	n/a	n/a
7	ETS1	chr6:56954492-56955164	K562	blood:	n/a	chr6:56954792-56954805 chr6:56954791-56954804
8	BCLAF1	chr6:56954456-56955077	GM12878	blood:	n/a	n/a
9	ZC3H11A	chr6:56954439-56954919	K562	blood:	n/a	n/a
10	POLR2A	chr6:56954384-56955093	HUVEC	blood vessel:	n/a	n/a
11	MYC	chr6:56954333-56955142	K562	blood:	n/a	n/a
12	TBP	chr6:56954510-56955074	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr6:56954494-56955199	NB4	blood:	n/a	n/a
14	TCF12	chr6:56954479-56955110	ECC-1	luminal epithelium:	n/a	chr6:56954725-56954732 chr6:56954694-56954701 chr6:56954693-56954703 chr6:56954504-56954513
15	CTCF	chr6:56954496-56954993	K562	blood:	n/a	n/a
16	RCOR1	chr6:56954363-56955123	K562	blood:	n/a	n/a
17	TAF1	chr6:56954499-56955073	H1-neurons	neurons:	n/a	n/a
18	NR2F2	chr6:56954064-56955216	K562	blood:	n/a	chr6:56954199-56954214
19	POLR2A	chr6:56954513-56954730	GM12891	blood:	n/a	n/a
20	GABPA	chr6:56954257-56955129	MCF-7	breast:	n/a	n/a
21	NFIC	chr6:56954406-56955094	HepG2	liver:	n/a	n/a
22	IRF1	chr6:56954445-56955077	K562	blood:	n/a	chr6:56954523-56954533 chr6:56954709-56954723 chr6:56954523-56954537 chr6:56954522-56954539 chr6:56954522-56954534 chr6:56954538-56954548 chr6:56954519-56954533
23	SP1	chr6:56954502-56955415	GM12878	blood:	n/a	chr6:56954712-56954722 chr6:56955255-56955267 chr6:56954712-56954722 chr6:56954711-56954722 chr6:56954711-56954723
24	TEAD4	chr6:56954336-56955375	HepG2	liver:	n/a	n/a
25	POLR2A	chr6:56954470-56956307	GM12891	blood:	n/a	n/a
26	POLR2A	chr6:56954400-56955479	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr6:56954443-56955131	K562	blood:	n/a	n/a
28	SP1	chr6:56954426-56955033	GM12878	blood:	n/a	chr6:56954712-56954722 chr6:56954712-56954722 chr6:56954711-56954722 chr6:56954711-56954723
29	POLR2A	chr6:56954299-56955197	PBDE	blood:	n/a	n/a
30	RAD21	chr6:56954482-56955096	H1-hESC	embryonic stem cell:	n/a	n/a
31	ELF1	chr6:56954484-56955054	MCF-7	breast:	n/a	n/a
32	HDAC2	chr6:56954503-56954862	K562	blood:	n/a	chr6:56954750-56954764 chr6:56954532-56954546 chr6:56954527-56954541 chr6:56954526-56954540 chr6:56954504-56954513
33	ZNF143	chr6:56954410-56955151	GM12878	blood:	n/a	chr6:56954797-56954816 chr6:56954793-56954811 chr6:56954793-56954802 chr6:56954795-56954804
34	POLR2A	chr6:56954376-56955507	SK-N-SH	brain:	n/a	n/a
35	ELF1	chr6:56954513-56955108	SK-N-SH	brain:	n/a	n/a
36	SP1	chr6:56954514-56955212	A549	lung:	n/a	chr6:56954712-56954722 chr6:56954712-56954722 chr6:56954711-56954722 chr6:56954711-56954723
37	MAX	chr6:56954455-56955107	HCT-116	colon:	n/a	n/a
38	MTA3	chr6:56954254-56955171	GM12878	blood:	n/a	n/a
39	EP300	chr6:56954472-56955030	HepG2	liver:	n/a	chr6:56954833-56954846 chr6:56954531-56954545
40	POLR2A	chr6:56954493-56955183	SK-N-SH	brain:	n/a	n/a
41	HCFC1	chr6:56954212-56955189	Hela-S3	cervix:	n/a	n/a
42	GATA1	chr6:56953499-56955181	PBDE	blood:	n/a	chr6:56954751-56954761 chr6:56953627-56953637
43	MAX	chr6:56954495-56955155	K562	blood:	n/a	n/a
44	POLR2A	chr6:56954285-56955139	GM12878	blood:	n/a	n/a
45	GABPA	chr6:56954488-56955121	HL-60	blood:	n/a	n/a
46	POLR2A	chr6:56954467-56955119	H1-neurons	neurons:	n/a	n/a
47	NFIC	chr6:56954375-56955207	GM12878	blood:	n/a	n/a
48	PML	chr6:56954300-56955174	K562	blood:	n/a	chr6:56954843-56954851
49	ELF1	chr6:56954437-56955104	HCT-116	colon:	n/a	n/a
50	RAD21	chr6:56954496-56955080	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:56954167..56956467-chr6:57034197..57037095,2	K562	blood:
2	chr6:56818718..56821144-chr6:56954189..56956169,2	MCF-7	breast:
3	chr6:56948909..56950719-chr6:56952712..56954669,2	K562	blood:
4	chr6:56911241..56911877-chr6:56954515..56955089,3	Hela-S3	cervix:

Variant related genes	Relation type
ZNF451	TF binding region
ENSG00000226803	Chromatin interaction
ENSG00000168116	Chromatin interaction
ENSG00000151917	Chromatin interaction
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1020550	0.90[ASN][1000 genomes]
rs1044670	0.88[CEU][hapmap]
rs10456192	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10484410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11398	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs12190575	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192222	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194288	0.90[ASN][1000 genomes]
rs12194407	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198801	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201039	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12211901	0.90[ASN][1000 genomes]
rs12214119	0.94[EUR][1000 genomes]
rs12214882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411578	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1547226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16888392	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17619360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800018	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs3800023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800025	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3957366	0.88[CEU][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs3996934	0.90[ASN][1000 genomes]
rs3996935	0.90[ASN][1000 genomes]
rs3996936	0.90[ASN][1000 genomes]
rs4523090	0.90[ASN][1000 genomes]
rs4631287	0.90[ASN][1000 genomes]
rs6902125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6918222	0.85[EUR][1000 genomes]
rs6936506	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72868608	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73463742	0.80[ASN][1000 genomes]
rs7744148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7748120	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7748453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7753547	0.90[ASN][1000 genomes]
rs7756421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7764446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7771115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349841	0.85[ASN][1000 genomes]
rs9396247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9396256	0.90[ASN][1000 genomes]
rs986245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][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	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv970717	chr6:56903957-56955783	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	esv3374787	chr6:56912959-56955113	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv350038	chr6:56953752-56960124	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6459178	RAB23	cis	lymphoblastoid	seeQTL
rs6459178	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL
rs6459178	BEND6	cis	parietal	SCAN
rs6459178	BEND6	cis	cerebellum	SCAN
rs6459178	BEND6	cis	Muscle Skeletal	GTEx
rs6459178	RAB23	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56927000-56954800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:56935200-56954800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:56953200-56954800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:56954000-56966800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:56954200-56954600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:56954200-56954600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:56954200-56954600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr6:56954200-56954600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:56954200-56954600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr6:56954200-56954600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr6:56954200-56954600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr6:56954200-56954600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:56954200-56954600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:56954200-56954600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:56954200-56954600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr6:56954200-56954600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr6:56954200-56954600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:56954200-56954600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:56954200-56954600	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr6:56954200-56954600	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr6:56954200-56954600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:56954200-56954600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr6:56954200-56954600	Flanking Active TSS	Fetal Heart	heart
24	chr6:56954200-56954600	Flanking Active TSS	Fetal Lung	lung
25	chr6:56954200-56954600	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr6:56954200-56954600	Flanking Active TSS	GM12878-XiMat	blood
27	chr6:56954200-56954600	Flanking Active TSS	Hela-S3	cervix
28	chr6:56954200-56954600	Flanking Active TSS	HepG2	liver
29	chr6:56954200-56954600	Flanking Active TSS	HSMMtube	muscle
30	chr6:56954200-56954600	Flanking Active TSS	K562	blood
31	chr6:56954200-56954600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr6:56954200-56954600	Flanking Active TSS	NHDF-Ad	bronchial
33	chr6:56954200-56954600	Flanking Active TSS	NHLF	lung
34	chr6:56954200-56954800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:56954200-56954800	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr6:56954200-56954800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:56954200-56954800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr6:56954200-56954800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr6:56954200-56954800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:56954200-56954800	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr6:56954200-56954800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr6:56954200-56954800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr6:56954200-56954800	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr6:56954200-56954800	Flanking Active TSS	Dnd41	blood
45	chr6:56954200-56954800	Flanking Active TSS	HUVEC	blood vessel
46	chr6:56954200-56954800	Flanking Active TSS	NHEK	skin
47	chr6:56954200-56954800	Flanking Active TSS	Osteobl	bone
48	chr6:56954200-56955000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:56954200-56955000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:56954200-56955200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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