Variant report

Variant	rs11754384
Chromosome Location	chr6:26322985-26322986
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:243)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:243 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr6:26322871-26323193	MCF10A-Er-Src	breast:	n/a	chr6:26322942-26322950
2	USF1	chr6:26322805-26323245	A549	lung:	n/a	chr6:26323046-26323057
3	RELA	chr6:26322870-26323563	GM18951	blood:	n/a	n/a
4	ZNF217	chr6:26322900-26323416	MCF-7	breast:	n/a	n/a
5	MAZ	chr6:26322225-26323447	Hela-S3	cervix:	n/a	n/a
6	USF1	chr6:26322805-26323163	SK-N-SH_RA	brain:	n/a	chr6:26323046-26323057
7	TBP	chr6:26322770-26323314	Hela-S3	cervix:	n/a	n/a
8	TBL1XR1	chr6:26322261-26323598	K562	blood:	n/a	n/a
9	YY1	chr6:26322811-26323575	SK-N-SH	brain:	n/a	n/a
10	TEAD4	chr6:26322193-26323759	HepG2	liver:	n/a	n/a
11	MXI1	chr6:26322689-26323418	K562	blood:	n/a	n/a
12	GTF2F1	chr6:26322942-26323640	K562	blood:	n/a	n/a
13	USF1	chr6:26322757-26323526	ECC-1	luminal epithelium:	n/a	chr6:26323046-26323057
14	USF1	chr6:26322769-26323442	A549	lung:	n/a	chr6:26323046-26323057
15	STAT5A	chr6:26322953-26323566	K562	blood:	n/a	n/a
16	REST	chr6:26322950-26323439	A549	lung:	n/a	n/a
17	YY1	chr6:26322724-26323548	ECC-1	luminal epithelium:	n/a	n/a
18	SP4	chr6:26322774-26323284	H1-hESC	embryonic stem cell:	n/a	n/a
19	ETS1	chr6:26322917-26323343	A549	lung:	n/a	n/a
20	MAX	chr6:26322345-26323519	A549	lung:	n/a	n/a
21	JUND	chr6:26322919-26323225	HepG2	liver:	n/a	n/a
22	TRIM28	chr6:26322053-26323670	K562	blood:	n/a	n/a
23	MAX	chr6:26322862-26323232	H1-hESC	embryonic stem cell:	n/a	n/a
24	PML	chr6:26322072-26323530	GM12878	blood:	n/a	n/a
25	TBL1XR1	chr6:26322293-26323565	K562	blood:	n/a	n/a
26	TCF12	chr6:26322075-26323530	A549	lung:	n/a	n/a
27	USF1	chr6:26322746-26323467	K562	blood:	n/a	chr6:26323046-26323057
28	RELA	chr6:26322762-26323267	GM12878	blood:	n/a	n/a
29	ELF1	chr6:26322861-26323411	HepG2	liver:	n/a	n/a
30	TEAD4	chr6:26322804-26323380	A549	lung:	n/a	n/a
31	NR2F2	chr6:26321928-26323880	K562	blood:	n/a	n/a
32	MAX	chr6:26322471-26323294	HepG2	liver:	n/a	n/a
33	MAX	chr6:26322767-26323468	MCF-7	breast:	n/a	n/a
34	FOSL2	chr6:26322822-26323276	HepG2	liver:	n/a	n/a
35	CEBPB	chr6:26322836-26323183	HepG2	liver:	n/a	n/a
36	YY1	chr6:26322226-26323113	GM12878	blood:	n/a	n/a
37	MAX	chr6:26322846-26323270	H1-hESC	embryonic stem cell:	n/a	n/a
38	SIN3AK20	chr6:26322128-26323669	MCF-7	breast:	n/a	n/a
39	YY1	chr6:26322896-26323391	SK-N-SH_RA	brain:	n/a	n/a
40	SP1	chr6:26322782-26323615	A549	lung:	n/a	n/a
41	KAP1	chr6:26322237-26323816	U2OS	brain:	n/a	n/a
42	ZNF143	chr6:26322982-26323299	GM12878	blood:	n/a	chr6:26323276-26323295
43	MAX	chr6:26322868-26323232	HUVEC	blood vessel:	n/a	n/a
44	MAX	chr6:26322130-26323482	HCT-116	colon:	n/a	n/a
45	JUND	chr6:26322833-26323343	H1-hESC	embryonic stem cell:	n/a	n/a
46	CHD2	chr6:26322930-26323491	K562	blood:	n/a	n/a
47	TBP	chr6:26322758-26323328	K562	blood:	n/a	n/a
48	EP300	chr6:26322794-26323303	GM12878	blood:	n/a	n/a
49	MAX	chr6:26322820-26323388	SK-N-SH	brain:	n/a	n/a
50	HCFC1	chr6:26322266-26323375	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226250046..226250889-chr6:26322132..26323073,2	NB4	blood:
2	chr6:26273199..26275817-chr6:26322608..26324495,2	MCF-7	breast:
3	chr6:26322866..26325773-chr6:26327005..26329096,3	MCF-7	breast:
4	chr6:26321606..26324992-chr6:26518176..26520933,3	K562	blood:

No data

Variant related genes	Relation type
HIST1H3PS1	TF binding region
ENSG00000163041	Chromatin interaction
ENSG00000199289	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11751564	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11751567	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11751978	0.85[CEU][hapmap]
rs11752014	0.85[CEU][hapmap]
rs11754168	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11754746	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11755795	1.00[CEU][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11756428	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11757214	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11757736	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11759682	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11962642	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16891523	0.85[CEU][hapmap]
rs16891525	0.85[CEU][hapmap]
rs1883214	0.85[CEU][hapmap]
rs2006005	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2006006	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34434694	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3823157	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41266829	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41266831	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4631273	0.85[CEU][hapmap]
rs56768418	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57145038	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57530446	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59225416	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60122474	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60228626	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61082103	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61213538	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61625476	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6901243	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6914596	0.85[CEU][hapmap]
rs6916643	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6938696	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73393491	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73393492	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73395313	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73395314	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73397320	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73397336	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73397339	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73397347	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73397364	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73399366	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73399394	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73401208	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73401228	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73401231	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73401236	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73401243	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7740838	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7761779	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7773163	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9688734	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers 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	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
6	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
7	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
8	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
9	nsv525347	chr6:26313348-26322985	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv969357	chr6:26321434-26323580	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv5230	chr6:26321593-26361531	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11754384	ZNF165	cis	parietal	SCAN
rs11754384	HIST1H3E	cis	cerebellum	SCAN
rs11754384	HIST1H3E	cis	parietal	SCAN
rs11754384	ZKSCAN4	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26318600-26323400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:26318800-26323200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:26319000-26323000	Active TSS	H1 Cell Line	embryonic stem cell
4	chr6:26319000-26323000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:26321200-26323000	Active TSS	HUVEC	blood vessel
6	chr6:26321200-26323800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:26321400-26323000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:26321400-26323000	Active TSS	HMEC	breast
9	chr6:26321400-26323200	Active TSS	HepG2	liver
10	chr6:26321400-26323400	Active TSS	GM12878-XiMat	blood
11	chr6:26321400-26323600	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr6:26321600-26323000	Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr6:26321600-26323000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:26321600-26323000	Active TSS	NHDF-Ad	bronchial
15	chr6:26321600-26323000	Active TSS	NHEK	skin
16	chr6:26321600-26323200	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr6:26321600-26323200	Active TSS	Hela-S3	cervix
18	chr6:26321600-26323200	Active TSS	K562	blood
19	chr6:26321600-26323400	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr6:26321600-26323600	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr6:26321600-26323600	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr6:26321600-26323600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:26321600-26323800	Active TSS	A549	lung
24	chr6:26321800-26323000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:26321800-26323000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:26321800-26323000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:26321800-26323000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:26321800-26323000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:26321800-26323000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:26321800-26323000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:26321800-26323000	Active TSS	Muscle Satellite Cultured Cells	--
32	chr6:26321800-26323000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:26321800-26323000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:26321800-26323000	Active TSS	Psoas Muscle	Psoas
35	chr6:26321800-26323000	Active TSS	Dnd41	blood
36	chr6:26321800-26323000	Active TSS	NH-A	brain
37	chr6:26321800-26323200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:26321800-26323400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:26321800-26323600	Active TSS	HSMM	muscle
40	chr6:26321800-26323800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:26322000-26323000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:26322000-26323000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:26322000-26323000	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr6:26322000-26323000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:26322000-26323000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:26322000-26323000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
47	chr6:26322000-26323000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:26322000-26323000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
49	chr6:26322000-26323000	Active TSS	Brain Anterior Caudate	brain
50	chr6:26322000-26323000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain

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