Variant report

Variant	rs9468168
Chromosome Location	chr6:27560236-27560237
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	ATF2	chr6:27560222-27560889	GM12878	blood:	n/a	n/a
2	PML	chr6:27560120-27561014	GM12878	blood:	n/a	n/a
3	HMGN3	chr6:27560207-27560775	K562	blood:	n/a	n/a
4	BHLHE40	chr6:27560016-27560994	K562	blood:	n/a	n/a
5	REST	chr6:27560076-27560941	K562	blood:	n/a	n/a
6	POLR2A	chr6:27559682-27561420	H1-neurons	neurons:	n/a	n/a
7	RPC155	chr6:27560186-27560885	Hela-S3	cervix:	n/a	n/a
8	SIN3A	chr6:27559517-27561282	H1-hESC	embryonic stem cell:	n/a	chr6:27561096-27561109
9	ELF1	chr6:27560231-27560799	HepG2	liver:	n/a	n/a
10	JUN	chr6:27560134-27560870	K562	blood:	n/a	n/a
11	CTCF	chr6:27560140-27560290	GM12878	blood:	n/a	n/a
12	CCNT2	chr6:27560140-27560939	K562	blood:	n/a	chr6:27560689-27560709
13	ATF3	chr6:27559169-27561107	A549	lung:	n/a	n/a
14	REST	chr6:27560178-27561082	PFSK-1	brain:	n/a	n/a
15	BCLAF1	chr6:27560119-27560892	K562	blood:	n/a	n/a
16	STAT5A	chr6:27560030-27560946	GM12878	blood:	n/a	chr6:27560187-27560196 chr6:27560188-27560197 chr6:27560188-27560211 chr6:27560185-27560199
17	MAX	chr6:27560125-27560840	ECC-1	luminal epithelium:	n/a	n/a
18	MYBL2	chr6:27560146-27561069	HepG2	liver:	n/a	n/a
19	MYC	chr6:27560044-27560770	MCF10A-Er-Src	breast:	n/a	n/a
20	NFIC	chr6:27560167-27560909	GM12878	blood:	n/a	n/a
21	TBL1XR1	chr6:27559329-27560883	K562	blood:	n/a	n/a
22	BCLAF1	chr6:27560111-27561123	GM12878	blood:	n/a	chr6:27561060-27561069
23	NFYA	chr6:27560074-27560295	K562	blood:	n/a	n/a
24	STAT3	chr6:27560082-27560355	MCF10A-Er-Src	breast:	n/a	chr6:27560187-27560196 chr6:27560188-27560197 chr6:27560186-27560197 chr6:27560188-27560211 chr6:27560185-27560199
25	TEAD4	chr6:27559243-27561438	K562	blood:	n/a	n/a
26	UBTF	chr6:27559528-27560776	K562	blood:	n/a	n/a
27	KAP1	chr6:27559407-27561228	HEK293	kidney:	n/a	n/a
28	STAT3	chr6:27559653-27560631	MCF10A-Er-Src	breast:	n/a	chr6:27560187-27560196 chr6:27560188-27560197 chr6:27560186-27560197 chr6:27560188-27560211 chr6:27560185-27560199
29	CBX3	chr6:27560157-27561050	HCT-116	colon:	n/a	n/a
30	RXRA	chr6:27560202-27560994	SK-N-SH	brain:	n/a	n/a
31	CBX3	chr6:27560222-27560873	K562	blood:	n/a	n/a
32	GTF3C2	chr6:27560067-27560791	Hela-S3	cervix:	n/a	n/a
33	MBD4	chr6:27560198-27561212	HepG2	liver:	n/a	n/a
34	POLR2A	chr6:27559692-27561541	H1-neurons	neurons:	n/a	n/a
35	STAT5A	chr6:27560225-27560815	GM12878	blood:	n/a	n/a
36	ATF3	chr6:27559238-27561015	K562	blood:	n/a	n/a
37	CBX3	chr6:27559260-27561263	K562	blood:	n/a	n/a
38	USF2	chr6:27560218-27560759	Hela-S3	cervix:	n/a	n/a
39	TCF7L2	chr6:27560141-27560680	HEK293	kidney:	n/a	n/a
40	STAT1	chr6:27560169-27560850	GM12878	blood:	n/a	chr6:27560187-27560196 chr6:27560188-27560197 chr6:27560188-27560211 chr6:27560185-27560199
41	ZNF217	chr6:27560235-27560962	MCF-7	breast:	n/a	n/a
42	FOS	chr6:27560069-27560632	MCF10A-Er-Src	breast:	n/a	n/a
43	ETS1	chr6:27560115-27561133	K562	blood:	n/a	chr6:27560437-27560444
44	MBD4	chr6:27560180-27560874	HepG2	liver:	n/a	n/a
45	GTF3C2	chr6:27559393-27560882	K562	blood:	n/a	n/a
46	ELF1	chr6:27560165-27560836	K562	blood:	n/a	n/a
47	ATF3	chr6:27560181-27561054	A549	lung:	n/a	n/a
48	STAT3	chr6:27559974-27560695	MCF10A-Er-Src	breast:	n/a	chr6:27560187-27560196 chr6:27560188-27560197 chr6:27560186-27560197 chr6:27560188-27560211 chr6:27560185-27560199
49	ATF2	chr6:27560052-27560803	GM12878	blood:	n/a	n/a
50	NR2F2	chr6:27560228-27560956	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:27558513..27562026-chr6:27562388..27564787,3	K562	blood:
2	chr6:27519483..27521116-chr6:27558602..27560332,2	K562	blood:
3	chr6:27485761..27488358-chr6:27559045..27561077,2	K562	blood:
4	chr6:27516649..27519121-chr6:27558606..27561383,2	K562	blood:
5	chr6:27549818..27556949-chr6:27557615..27563432,7	K562	blood:
6	chr6:27549715..27554180-chr6:27555593..27563261,8	K562	blood:
7	chr6:27560152..27562900-chr6:28715549..28717321,2	K562	blood:
8	chr6:27558583..27561214-chr6:27719565..27721812,2	K562	blood:
9	chr6:27559085..27561066-chr6:27755940..27758239,2	K562	blood:
10	chr6:27558513..27561961-chr6:27562522..27566444,4	K562	blood:
11	chr6:27559025..27560718-chr6:27653331..27656285,2	K562	blood:
12	chr6:27513701..27516143-chr6:27559137..27561028,2	K562	blood:

Variant related genes	Relation type
RNU6-471P	TF binding region
ENSG00000206671	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs16867857	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2056923	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2064092	0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6903982	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6907861	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72500859	0.86[ASN][1000 genomes]
rs9468149	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9468152	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9468153	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9468154	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9468155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9468159	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9468174	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv1017347	chr6:27483816-27605842	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025572	chr6:27487852-27604454	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv538167	chr6:27487852-27604454	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv883509	chr6:27492906-27586181	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1018107	chr6:27503525-27596736	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv538168	chr6:27503525-27596736	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27559200-27560800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:27559200-27560800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr6:27559400-27560400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
4	chr6:27559400-27560800	Active TSS	H1 Cell Line	embryonic stem cell
5	chr6:27559400-27560800	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:27559400-27560800	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr6:27559400-27560800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:27559400-27560800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
9	chr6:27559400-27560800	Active TSS	K562	blood
10	chr6:27559400-27561000	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr6:27559400-27561200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr6:27559400-27561200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:27559600-27560400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
14	chr6:27559600-27560600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:27559600-27560600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
16	chr6:27559600-27560600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:27559600-27560600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
18	chr6:27559600-27560600	Active TSS	GM12878-XiMat	blood
19	chr6:27559600-27560800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:27559600-27560800	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr6:27559600-27560800	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr6:27559600-27560800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:27559600-27560800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:27559600-27560800	Flanking Active TSS	HUVEC	blood vessel
25	chr6:27559600-27561000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:27559600-27561000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:27559600-27561000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:27559600-27561000	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr6:27559600-27561000	Active TSS	NH-A	brain
30	chr6:27559600-27561200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:27559600-27561400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:27559600-27561400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:27559600-27561400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:27559600-27561600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
35	chr6:27559600-27561600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:27559600-27561800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:27559600-27562000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:27559600-27562200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:27559600-27562200	Active TSS	A549	lung
40	chr6:27559600-27562600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:27559600-27562800	Active TSS	H9 Cell Line	embryonic stem cell
42	chr6:27559800-27560400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
43	chr6:27559800-27560400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:27559800-27560600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:27559800-27560600	Active TSS	Placenta	Placenta
46	chr6:27559800-27560600	Active TSS	Placenta Amnion	Placenta Amnion
47	chr6:27559800-27560800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
48	chr6:27559800-27560800	Bivalent/Poised TSS	Fetal Lung	lung
49	chr6:27559800-27560800	Active TSS	HSMMtube	muscle
50	chr6:27559800-27561000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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