Variant report

Variant	rs13203681
Chromosome Location	chr6:56706159-56706160
allele	A/T
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	POLR2A	chr6:56705597-56706168	H1-neurons	neurons:	n/a	n/a
2	FOSL2	chr6:56705607-56706228	SK-N-SH	brain:	n/a	n/a
3	MAFK	chr6:56705651-56706327	IMR90	lung:	n/a	chr6:56706140-56706151 chr6:56706139-56706153
4	GATA3	chr6:56705516-56706305	SK-N-SH	brain:	n/a	chr6:56705660-56705667
5	MAX	chr6:56705821-56706182	SK-N-SH	brain:	n/a	n/a
6	STAT3	chr6:56705687-56706190	MCF10A-Er-Src	breast:	n/a	chr6:56706077-56706088 chr6:56705981-56705992
7	REST	chr6:56705493-56707112	H1-neurons	neurons:	n/a	chr6:56707056-56707069
8	FOSL1	chr6:56705633-56706281	HCT-116	colon:	n/a	n/a
9	POLR2A	chr6:56705527-56706173	SK-N-SH	brain:	n/a	n/a
10	JUN	chr6:56705669-56706179	HUVEC	blood vessel:	n/a	n/a
11	JUN	chr6:56705642-56706162	Hela-S3	cervix:	n/a	n/a
12	JUND	chr6:56705395-56706266	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr6:56705886-56706207	ProgFib	skin:	n/a	n/a
14	POLR2A	chr6:56705743-56706224	IMR90	lung:	n/a	n/a
15	POLR2A	chr6:56705677-56706159	H1-neurons	neurons:	n/a	n/a
16	MAFK	chr6:56705646-56706346	Hela-S3	cervix:	n/a	chr6:56706140-56706151 chr6:56706139-56706153
17	MAFK	chr6:56705969-56706313	K562	blood:	n/a	chr6:56706140-56706151 chr6:56706139-56706153
18	CHD1	chr6:56704985-56709414	IMR90	lung:	n/a	n/a
19	JUND	chr6:56705549-56706227	SK-N-SH	brain:	n/a	n/a
20	GATA3	chr6:56705318-56706319	SK-N-SH	brain:	n/a	chr6:56705660-56705667
21	PBX3	chr6:56705447-56706198	SK-N-SH	brain:	n/a	n/a
22	NFIC	chr6:56705341-56706265	SK-N-SH	brain:	n/a	n/a
23	MAFK	chr6:56705957-56706320	HepG2	liver:	n/a	chr6:56706140-56706151 chr6:56706139-56706153
24	MAFK	chr6:56705955-56706313	HepG2	liver:	n/a	chr6:56706140-56706151 chr6:56706139-56706153
25	POLR2A	chr6:56705429-56706165	U87	brain:	n/a	n/a
26	KAP1	chr6:56705651-56706338	HEK293	kidney:	n/a	n/a
27	KAP1	chr6:56705615-56706161	U2OS	brain:	n/a	n/a
28	TCF12	chr6:56705303-56706342	SK-N-SH	brain:	n/a	chr6:56705397-56705406
29	MXI1	chr6:56705418-56706495	GM12878	blood:	n/a	chr6:56706374-56706383
30	TCF12	chr6:56705401-56706303	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr6:56705757-56706278	PANC-1	pancreas:	n/a	n/a
32	PBX3	chr6:56705406-56706260	SK-N-SH	brain:	n/a	n/a
33	SP1	chr6:56705550-56706228	HCT-116	colon:	n/a	n/a
34	POLR2A	chr6:56705647-56706165	U87	brain:	n/a	n/a
35	STAT3	chr6:56705700-56706165	Hela-S3	cervix:	n/a	chr6:56706077-56706088 chr6:56705981-56705992
36	POLR2A	chr6:56705671-56706871	PANC-1	pancreas:	n/a	n/a
37	EP300	chr6:56705575-56706256	SK-N-SH	brain:	n/a	n/a
38	MAFF	chr6:56705982-56706259	K562	blood:	n/a	n/a
39	MAFF	chr6:56705865-56706308	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:56683662..56685940-chr6:56704272..56706946,2	MCF-7	breast:
2	chr6:56702437..56704205-chr6:56705017..56706715,2	MCF-7	breast:
3	chr6:56702761..56706423-chr6:56707121..56709805,6	MCF-7	breast:
4	chr6:56704167..56710132-chr6:56712428..56720773,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231441	TF binding region
ENSG00000231441	Chromatin interaction
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10498812	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10498813	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11756551	0.85[EUR][1000 genomes]
rs11968575	0.81[CEU][hapmap]
rs11970648	1.00[CEU][hapmap]
rs13190854	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13192540	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13192931	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13194625	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13194904	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13195601	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13198204	0.89[EUR][1000 genomes]
rs13198597	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13200166	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13200559	0.84[EUR][1000 genomes]
rs13200768	0.88[EUR][1000 genomes]
rs13200868	0.82[EUR][1000 genomes]
rs13201639	0.89[EUR][1000 genomes]
rs13201733	0.89[EUR][1000 genomes]
rs13203000	0.81[CEU][hapmap]
rs13203148	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13203327	0.85[EUR][1000 genomes]
rs13204466	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13205667	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13207768	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13208409	0.81[EUR][1000 genomes]
rs13211879	0.94[EUR][1000 genomes]
rs13214893	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13215883	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13217390	0.81[CEU][hapmap]
rs13218913	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13220618	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13220628	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13220851	0.91[EUR][1000 genomes]
rs1610156	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1610157	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16888171	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs16888184	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16888186	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17684730	0.89[EUR][1000 genomes]
rs17684748	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17684772	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17684784	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17684802	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17684878	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17684884	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17684941	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17751966	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17751977	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17752002	0.89[EUR][1000 genomes]
rs17752046	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17752106	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17752213	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1903332	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28360570	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3002010	0.81[CEU][hapmap]
rs3002011	0.81[CEU][hapmap]
rs34083827	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34171958	0.90[EUR][1000 genomes]
rs34228698	0.89[EUR][1000 genomes]
rs34359353	0.90[EUR][1000 genomes]
rs34425815	0.88[EUR][1000 genomes]
rs34500949	0.84[EUR][1000 genomes]
rs34520435	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34612783	0.88[EUR][1000 genomes]
rs34614087	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34640766	0.89[EUR][1000 genomes]
rs34866877	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34896026	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34966024	0.83[EUR][1000 genomes]
rs35073881	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35080938	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35081015	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35225175	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35242294	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35251663	0.88[EUR][1000 genomes]
rs35407078	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35439100	0.97[EUR][1000 genomes]
rs35440408	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35440822	0.90[EUR][1000 genomes]
rs35461301	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35566812	0.87[EUR][1000 genomes]
rs35609883	0.89[EUR][1000 genomes]
rs35642890	0.89[EUR][1000 genomes]
rs35696739	0.89[EUR][1000 genomes]
rs35828379	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35851452	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35873865	0.87[EUR][1000 genomes]
rs35886823	0.89[EUR][1000 genomes]
rs35986172	0.81[EUR][1000 genomes]
rs36022925	0.89[EUR][1000 genomes]
rs36037734	0.89[EUR][1000 genomes]
rs36094082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4299824	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4348308	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4371846	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4415160	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4457154	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4532444	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4587171	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs56037312	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56368885	0.82[EUR][1000 genomes]
rs58980183	0.82[EUR][1000 genomes]
rs59432342	0.89[EUR][1000 genomes]
rs61601344	0.89[EUR][1000 genomes]
rs62411366	0.82[EUR][1000 genomes]
rs62411367	0.84[EUR][1000 genomes]
rs62411372	0.88[EUR][1000 genomes]
rs62411375	0.88[EUR][1000 genomes]
rs62411376	0.89[EUR][1000 genomes]
rs6904535	0.84[EUR][1000 genomes]
rs6905603	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6910414	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6914293	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6918949	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6928104	0.82[EUR][1000 genomes]
rs6934714	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71564854	0.89[EUR][1000 genomes]
rs71564855	0.90[EUR][1000 genomes]
rs71564856	0.89[EUR][1000 genomes]
rs71564861	0.89[EUR][1000 genomes]
rs71564863	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7758867	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7761501	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7761729	1.00[CEU][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7766565	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7771085	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7775182	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56702600-56706600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:56703000-56707200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:56703800-56706200	Enhancers	Rectal Smooth Muscle	rectum
4	chr6:56703800-56706400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:56704000-56706400	Active TSS	Psoas Muscle	Psoas
6	chr6:56704000-56709400	Active TSS	Right Atrium	heart
7	chr6:56704200-56707400	Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr6:56704200-56707600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:56704200-56709200	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr6:56704600-56709200	Active TSS	HSMMtube	muscle
11	chr6:56704800-56706800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:56704800-56706800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:56704800-56709400	Active TSS	HSMM	muscle
14	chr6:56705000-56709400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr6:56705200-56706200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:56705200-56706600	Active TSS	Brain Hippocampus Middle	brain
17	chr6:56705200-56707000	Flanking Active TSS	NH-A	brain
18	chr6:56705200-56707400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:56705200-56707400	Flanking Active TSS	Osteobl	bone
20	chr6:56705200-56709400	Active TSS	Right Ventricle	heart
21	chr6:56705400-56706200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr6:56705400-56706400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr6:56705400-56706400	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr6:56705400-56706600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:56705400-56707200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr6:56705400-56707400	Active TSS	Fetal Muscle Leg	muscle
27	chr6:56705400-56707600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:56705400-56707600	Active TSS	Fetal Muscle Trunk	muscle
29	chr6:56705400-56708000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:56705400-56708000	Flanking Active TSS	HUVEC	blood vessel
31	chr6:56705400-56709200	Active TSS	Brain Cingulate Gyrus	brain
32	chr6:56705400-56709200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:56705600-56706200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr6:56705600-56706200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:56705600-56706200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr6:56705600-56706200	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr6:56705600-56706200	Flanking Active TSS	GM12878-XiMat	blood
38	chr6:56705600-56706200	Enhancers	NHEK	skin
39	chr6:56705600-56706400	Enhancers	Hela-S3	cervix
40	chr6:56705600-56706600	Flanking Active TSS	HMEC	breast
41	chr6:56705600-56706800	Flanking Active TSS	Fetal Brain Male	brain
42	chr6:56705600-56707600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr6:56705600-56707600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:56705600-56707600	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr6:56705600-56708200	Active TSS	Fetal Heart	heart
46	chr6:56705600-56709200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr6:56705600-56709200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:56705600-56709200	Active TSS	Aorta	Aorta
49	chr6:56705600-56709200	Active TSS	Left Ventricle	heart
50	chr6:56705600-56709200	Active TSS	Stomach Smooth Muscle	stomach

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