Variant report

Variant	rs9368536
Chromosome Location	chr6:27840425-27840426
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:90)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:90 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27838549-27841707	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr6:27838747-27841649	PBDE	blood:	n/a	n/a
3	CHD1	chr6:27839408-27841329	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:27839297-27840460	MCF10A-Er-Src	breast:	n/a	n/a
5	BRCA1	chr6:27839944-27840724	H1-hESC	embryonic stem cell:	n/a	n/a
6	MTA3	chr6:27838567-27841844	GM12878	blood:	n/a	n/a
7	SP1	chr6:27839722-27840445	A549	lung:	n/a	chr6:27840162-27840183
8	RELA	chr6:27838795-27841703	GM10847	blood:	n/a	n/a
9	SP1	chr6:27839698-27840431	GM12878	blood:	n/a	chr6:27840162-27840183
10	NFIC	chr6:27839175-27841922	GM12878	blood:	n/a	n/a
11	RELA	chr6:27839203-27841750	GM18505	blood:	n/a	n/a
12	POLR2A	chr6:27839125-27840442	U87	brain:	n/a	n/a
13	POLR2A	chr6:27838660-27841777	GM12891	blood:	n/a	n/a
14	POLR2A	chr6:27838603-27840485	MCF-7	breast:	n/a	n/a
15	CEBPB	chr6:27839465-27840507	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:27838847-27841489	GM12892	blood:	n/a	n/a
17	POLR2A	chr6:27840368-27841478	GM12892	blood:	n/a	n/a
18	IRF4	chr6:27840401-27841431	GM12878	blood:	n/a	n/a
19	SP1	chr6:27839817-27840476	A549	lung:	n/a	chr6:27840162-27840183
20	ATF2	chr6:27840407-27841465	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:27838335-27841780	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr6:27839052-27841717	HUVEC	blood vessel:	n/a	n/a
23	CUX1	chr6:27840241-27840925	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:27838719-27841562	GM18951	blood:	n/a	n/a
25	POLR2A	chr6:27838702-27841553	GM19099	blood:	n/a	n/a
26	GATA1	chr6:27838875-27842026	PBDE	blood:	n/a	chr6:27839447-27839463 chr6:27839450-27839460 chr6:27839451-27839460 chr6:27839449-27839461
27	POLR2A	chr6:27838742-27841834	HUVEC	blood vessel:	n/a	n/a
28	JUND	chr6:27839715-27840736	H1-hESC	embryonic stem cell:	n/a	chr6:27840171-27840180
29	POLR2A	chr6:27838793-27841503	GM10847	blood:	n/a	n/a
30	TAF7	chr6:27838090-27841565	H1-hESC	embryonic stem cell:	n/a	n/a
31	CHD1	chr6:27838503-27841785	H1-hESC	embryonic stem cell:	n/a	n/a
32	NFIC	chr6:27839231-27841620	GM12878	blood:	n/a	n/a
33	BCLAF1	chr6:27839071-27841811	GM12878	blood:	n/a	chr6:27839452-27839459
34	POLR2A	chr6:27840418-27841436	GM12891	blood:	n/a	n/a
35	POLR2A	chr6:27838856-27841505	GM15510	blood:	n/a	n/a
36	POLR2A	chr6:27838729-27841503	GM18505	blood:	n/a	n/a
37	SP1	chr6:27839885-27840745	H1-hESC	embryonic stem cell:	n/a	chr6:27840162-27840183
38	CREB1	chr6:27838838-27840469	H1-hESC	embryonic stem cell:	n/a	n/a
39	ELF1	chr6:27839569-27840498	MCF-7	breast:	n/a	n/a
40	EP300	chr6:27839652-27841775	SK-N-SH	brain:	n/a	chr6:27840462-27840476 chr6:27840505-27840519 chr6:27840301-27840315
41	POLR2A	chr6:27838927-27841534	NB4	blood:	n/a	n/a
42	POLR2A	chr6:27838875-27841499	IMR90	lung:	n/a	n/a
43	POLR2A	chr6:27840406-27841394	H1-neurons	neurons:	n/a	n/a
44	POLR2A	chr6:27839015-27841605	U87	brain:	n/a	n/a
45	POLR2A	chr6:27838811-27841646	HUVEC	blood vessel:	n/a	n/a
46	RUNX3	chr6:27839189-27841805	GM12878	blood:	n/a	n/a
47	SP1	chr6:27839632-27840468	H1-hESC	embryonic stem cell:	n/a	chr6:27840162-27840183
48	POLR2A	chr6:27839097-27840577	HL-60	blood:	n/a	n/a
49	REST	chr6:27839415-27840580	H1-neurons	neurons:	n/a	n/a
50	ATF2	chr6:27838613-27841780	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26053886..26056754-chr6:27838528..27841562,3	MCF-7	breast:
2	chr1:149813872..149815940-chr6:27838697..27841107,2	MCF-7	breast:
3	chr6:26044692..26047309-chr6:27838299..27842021,15	MCF-7	breast:
4	chr17:57914621..57917067-chr6:27838760..27840646,2	MCF-7	breast:
5	chr1:68150557..68151470-chr6:27840179..27840812,2	NB4	blood:
6	chr16:88752577..88753488-chr6:27839952..27840679,2	NB4	blood:
7	chr6:26031607..26034880-chr6:27837430..27841431,3	K562	blood:
8	chr6:26044526..26047786-chr6:27838310..27841317,7	MCF-7	breast:
9	chr6:27838398..27840922-chr8:145149536..145152050,2	MCF-7	breast:
10	chr6:26055713..26057538-chr6:27839787..27841318,2	MCF-7	breast:
11	chr1:16839419..16842042-chr6:27838981..27840921,2	MCF-7	breast:
12	chr6:26123538..26126463-chr6:27839841..27841380,2	MCF-7	breast:
13	chr6:26025188..26029060-chr6:27836295..27841543,4	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H3I	TF binding region
ENSG00000261135	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000183558	Chromatin interaction
ENSG00000220323	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000196532	Chromatin interaction
ENSG00000179091	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000116717	Chromatin interaction
ENSG00000185669	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1010261	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs1015075	0.85[JPT][hapmap]
rs12174918	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16867962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs169287	0.91[ASN][1000 genomes]
rs175597	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17693877	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs183225	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs200466	0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs200469	1.00[JPT][hapmap]
rs200471	0.81[ASN][1000 genomes]
rs200473	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs200478	0.81[ASN][1000 genomes]
rs200479	0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs200481	0.87[ASN][1000 genomes]
rs200482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs200483	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs200484	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs200485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs200488	0.95[ASN][1000 genomes]
rs200489	0.95[ASN][1000 genomes]
rs200490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs200497	0.93[ASN][1000 genomes]
rs200498	0.91[ASN][1000 genomes]
rs200499	0.89[ASN][1000 genomes]
rs200501	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs200948	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs200949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs200950	1.00[ASN][1000 genomes]
rs200952	1.00[ASN][1000 genomes]
rs200953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs200954	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs200964	0.91[ASN][1000 genomes]
rs200965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs200966	0.91[ASN][1000 genomes]
rs200968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs200973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs200974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs200975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs200976	0.91[ASN][1000 genomes]
rs200977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs200979	0.93[ASN][1000 genomes]
rs200980	0.93[ASN][1000 genomes]
rs200981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs200983	0.95[ASN][1000 genomes]
rs200989	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs200990	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs200992	0.93[ASN][1000 genomes]
rs200995	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs200996	0.95[ASN][1000 genomes]
rs201002	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2277104	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2394001	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2747054	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34295134	0.95[ASN][1000 genomes]
rs36108923	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs370155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs390764	0.93[ASN][1000 genomes]
rs401754	0.93[ASN][1000 genomes]
rs401763	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4711161	1.00[EUR][1000 genomes]
rs4713117	1.00[EUR][1000 genomes]
rs4713122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4713124	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4713127	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs483143	0.88[ASN][1000 genomes]
rs493161	0.98[ASN][1000 genomes]
rs494887	0.93[ASN][1000 genomes]
rs557042	0.98[ASN][1000 genomes]
rs56870390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59015666	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs666846	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs904142	0.85[JPT][hapmap]
rs9348779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9368531	0.93[ASN][1000 genomes]
rs9368534	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9368535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368537	0.85[JPT][hapmap]
rs9380009	1.00[EUR][1000 genomes]
rs9380013	1.00[EUR][1000 genomes]
rs9380014	1.00[EUR][1000 genomes]
rs9380015	1.00[EUR][1000 genomes]
rs9380018	0.87[ASN][1000 genomes]
rs9380026	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380028	0.85[JPT][hapmap]
rs9380030	0.85[JPT][hapmap]
rs9380045	1.00[CEU][hapmap]
rs9393845	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs9393854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs9393855	1.00[EUR][1000 genomes]
rs9393858	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9393862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9393866	0.84[AMR][1000 genomes]
rs9468271	1.00[CEU][hapmap]
rs9468275	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
3	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
4	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
5	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27838200-27842000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr6:27838600-27842400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr6:27838800-27840800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:27838800-27841000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:27838800-27841400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:27838800-27842400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:27839000-27840800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:27839000-27841400	Active TSS	H1 Cell Line	embryonic stem cell
9	chr6:27839000-27841400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr6:27839000-27841400	Active TSS	Fetal Kidney	kidney
11	chr6:27839000-27841600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:27839000-27842200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:27839000-27842200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:27839000-27842400	Active TSS	Thymus	Thymus
15	chr6:27839000-27842800	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr6:27839200-27840600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:27839200-27840800	Active TSS	NHLF	lung
18	chr6:27839200-27841400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:27839200-27841400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:27839200-27841600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:27839200-27841600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:27839200-27841800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:27839200-27842000	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr6:27839200-27842200	Active TSS	H9 Cell Line	embryonic stem cell
25	chr6:27839400-27840600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:27839400-27841200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:27839400-27841200	Active TSS	A549	lung
28	chr6:27839400-27841400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:27839400-27841600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:27839400-27841600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:27839400-27841600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:27839400-27841800	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr6:27839400-27841800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
34	chr6:27839400-27841800	Active TSS	Fetal Brain Female	brain
35	chr6:27839400-27842000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr6:27839600-27841000	Active TSS	Aorta	Aorta
37	chr6:27839600-27841000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
38	chr6:27839600-27841000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:27839600-27841000	Bivalent/Poised TSS	Brain Substantia Nigra	brain
40	chr6:27839600-27841000	Active TSS	Gastric	stomach
41	chr6:27839600-27841400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:27839600-27841400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
43	chr6:27839600-27841400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
44	chr6:27839600-27841800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
45	chr6:27839600-27841800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
46	chr6:27839600-27841800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
47	chr6:27839800-27840600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr6:27839800-27840600	Active TSS	Fetal Muscle Leg	muscle
49	chr6:27839800-27840600	Active TSS	Fetal Thymus	thymus
50	chr6:27839800-27840600	Active TSS	Ovary	ovary

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