Variant report

Variant	rs483536
Chromosome Location	chr6:44235853-44235854
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	RAD21	chr6:44235547-44236523	SK-N-SH	brain:	n/a	chr6:44235925-44235944 chr6:44235778-44235790
2	CTCF	chr6:44235746-44236083	Medullo	brain:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
3	CTCF	chr6:44235840-44235990	BE2_C	brain:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
4	ARID3A	chr6:44235791-44236001	HepG2	liver:	n/a	n/a
5	CTCF	chr6:44235799-44236058	MCF-7	breast:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
6	CTCF	chr6:44235840-44235990	GM12866	blood:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
7	WRNIP1	chr6:44235779-44236101	GM12878	blood:	n/a	n/a
8	CTCF	chr6:44235820-44235970	HUVEC	blood vessel:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
9	CTCF	chr6:44235784-44236089	T-47D	breast:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
10	CTCF	chr6:44235820-44236002	SK-N-SH_RA	brain:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
11	SIN3AK20	chr6:44235759-44236330	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr6:44235740-44236087	T-47D	breast:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
13	RAD21	chr6:44235823-44236061	K562	blood:	n/a	chr6:44235925-44235944
14	RAD21	chr6:44235587-44236200	A549	lung:	n/a	chr6:44235925-44235944 chr6:44235778-44235790
15	CTCF	chr6:44235779-44236113	HepG2	liver:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
16	RAD21	chr6:44235742-44236142	IMR90	lung:	n/a	chr6:44235925-44235944 chr6:44235778-44235790
17	NFIC	chr6:44235582-44236181	ECC-1	luminal epithelium:	n/a	n/a
18	RAD21	chr6:44235823-44236079	GM12878	blood:	n/a	chr6:44235925-44235944
19	CTCF	chr6:44235694-44236173	H1-hESC	embryonic stem cell:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
20	CTCF	chr6:44235792-44236067	Hela-S3	cervix:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
21	RAD21	chr6:44235732-44236087	GM12878	blood:	n/a	chr6:44235925-44235944 chr6:44235778-44235790
22	ZNF143	chr6:44235772-44236098	Hela-S3	cervix:	n/a	n/a
23	MAX	chr6:44235730-44236098	K562	blood:	n/a	n/a
24	CTCF	chr6:44235790-44236109	GM19240	blood:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
25	ZNF143	chr6:44235742-44236127	GM12878	blood:	n/a	n/a
26	CTCF	chr6:44235679-44236145	K562	blood:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
27	CTCF	chr6:44235791-44236059	ProgFib	skin:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
28	CTCF	chr6:44235809-44236047	H1-hESC	embryonic stem cell:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
29	CTCF	chr6:44235624-44236139	IMR90	lung:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
30	SIN3A	chr6:44235722-44236699	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr6:44235820-44235970	NB4	blood:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
32	CTCF	chr6:44235840-44235990	GM12869	blood:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
33	CTCF	chr6:44235703-44236141	GM12878	blood:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
34	JUND	chr6:44235782-44236096	HepG2	liver:	n/a	chr6:44235942-44235952 chr6:44235942-44235952 chr6:44235942-44235952 chr6:44235942-44235952 chr6:44235943-44235951 chr6:44235941-44235953
35	TCF3	chr6:44235735-44236106	GM12878	blood:	n/a	n/a
36	RAD21	chr6:44235709-44236172	ECC-1	luminal epithelium:	n/a	chr6:44235925-44235944 chr6:44235778-44235790
37	CTCF	chr6:44235801-44236067	Fibrobl	skin:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
38	ATF2	chr6:44235700-44236137	H1-hESC	embryonic stem cell:	n/a	n/a
39	SMC3	chr6:44235739-44236162	Hela-S3	cervix:	n/a	n/a
40	USF2	chr6:44235810-44236038	Hela-S3	cervix:	n/a	chr6:44235924-44235935
41	CTCF	chr6:44235820-44235970	Hela-S3	cervix:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
42	CTCF	chr6:44235840-44235990	RPTEC	kidney:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
43	CTCF	chr6:44235752-44236147	K562	blood:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
44	RAD21	chr6:44235709-44236262	MCF-7	breast:	n/a	chr6:44235925-44235944 chr6:44235778-44235790
45	SP4	chr6:44235766-44236141	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr6:44235696-44236110	ECC-1	luminal epithelium:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
47	RCOR1	chr6:44235768-44236102	HepG2	liver:	n/a	n/a
48	CTCF	chr6:44235820-44235970	HCM	heart:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
49	MYC	chr6:44235797-44236160	H1-hESC	embryonic stem cell:	n/a	n/a
50	TCF3	chr6:44235763-44236038	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:44229152..44231602-chr6:44233591..44236343,2	MCF-7	breast:
2	chr6:44235432..44236394-chr6:44272155..44273117,4	MCF-7	breast:
3	chr6:43857455..43859614-chr6:44235657..44237353,2	K562	blood:
4	chr6:44235250..44236905-chr6:44304916..44306810,16	MCF-7	breast:
5	chr6:44235757..44236368-chr6:44272215..44272871,2	K562	blood:
6	chr6:44235516..44236382-chr6:44423771..44424641,3	K562	blood:
7	chr6:44234643..44237474-chr6:44296098..44297940,2	MCF-7	breast:
8	chr6:44235419..44235959-chr6:44307130..44307772,2	MCF-7	breast:
9	chr6:44233082..44237547-chr6:44353791..44357282,5	MCF-7	breast:
10	chr6:44235463..44235997-chr6:44306301..44306808,2	MCF-7	breast:
11	chr6:44234588..44237594-chr6:44277478..44280850,3	MCF-7	breast:
12	chr6:44235750..44236849-chr6:44272248..44273140,3	MCF-7	breast:
13	chr6:44084290..44087287-chr6:44233720..44236514,2	K562	blood:
14	chr6:44235852..44236696-chr6:44437202..44438131,2	MCF-7	breast:
15	chr6:44235214..44237013-chr6:44305028..44307078,2	MCF-7	breast:
16	chr6:44233695..44236268-chr6:44306586..44308563,3	K562	blood:
17	chr6:44235278..44236426-chr6:44305941..44306986,11	K562	blood:
18	chr6:44235532..44236481-chr6:44305932..44306869,8	MCF-7	breast:

Variant related genes	Relation type
TMEM151B	TF binding region
NFKBIE	TF binding region
ENSG00000096401	Chromatin interaction

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

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

rs_ID	r²[population]
rs1283567	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2233437	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs324137	0.86[JPT][hapmap]
rs325000	0.82[JPT][hapmap]
rs325001	0.86[JPT][hapmap]
rs3799962	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs498512	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs513688	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs524533	0.82[CEU][hapmap]
rs545970	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs571770	0.82[CEU][hapmap]
rs639728	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs651297	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs730775	0.95[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	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv885851	chr6:44178471-44240559	Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
3	nsv603003	chr6:44191920-44253765	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
7	nsv524398	chr6:44200953-44253765	Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv885854	chr6:44211867-44274797	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
9	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
10	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
11	nsv885857	chr6:44223010-44250165	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44233000-44236000	Weak transcription	Fetal Heart	heart
2	chr6:44233400-44236000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr6:44233400-44236000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:44233400-44236200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:44233400-44236200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:44233400-44237000	Weak transcription	HMEC	breast
7	chr6:44233400-44237200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:44233400-44237400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:44233400-44237800	Weak transcription	Pancreas	Pancrea
10	chr6:44233400-44237800	Weak transcription	Right Ventricle	heart
11	chr6:44233600-44236000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:44233600-44236000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:44233600-44236000	Weak transcription	Fetal Brain Male	brain
14	chr6:44233600-44236000	Weak transcription	Fetal Brain Female	brain
15	chr6:44233600-44236200	Weak transcription	Brain Substantia Nigra	brain
16	chr6:44233600-44238000	Weak transcription	Right Atrium	heart
17	chr6:44233800-44236000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:44233800-44236000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:44233800-44236000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:44234000-44236000	Enhancers	Primary B cells from peripheral blood	blood
21	chr6:44234600-44237200	Weak transcription	Spleen	Spleen
22	chr6:44234800-44238000	Enhancers	GM12878-XiMat	blood
23	chr6:44235400-44237800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr6:44235600-44236000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr6:44235600-44236000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:44235600-44236000	Enhancers	Fetal Thymus	thymus
27	chr6:44235600-44236400	Bivalent Enhancer	Fetal Muscle Leg	muscle
28	chr6:44235600-44236400	Bivalent Enhancer	HepG2	liver
29	chr6:44235800-44236200	Enhancers	Brain Anterior Caudate	brain
30	chr6:44235800-44236200	Bivalent Enhancer	Thymus	Thymus
31	chr6:44235800-44236400	Enhancers	Brain Hippocampus Middle	brain
32	chr6:44235800-44236400	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr6:44235800-44236400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:44235800-44236600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:44235800-44236600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:44235800-44236600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr6:44235800-44237600	Enhancers	Brain Germinal Matrix	brain

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