Variant report

Variant	rs513688
Chromosome Location	chr6:44235690-44235691
allele	G/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	RAD21	chr6:44235587-44236200	A549	lung:	n/a	chr6:44235925-44235944 chr6:44235778-44235790
3	NFIC	chr6:44235582-44236181	ECC-1	luminal epithelium:	n/a	n/a
4	CTCF	chr6:44235679-44236145	K562	blood:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
5	CTCF	chr6:44235624-44236139	IMR90	lung:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
6	RUNX3	chr6:44235685-44236153	GM12878	blood:	n/a	n/a
7	RAD21	chr6:44235650-44236161	MCF-7	breast:	n/a	chr6:44235925-44235944 chr6:44235778-44235790
8	CTCF	chr6:44235682-44236113	K562	blood:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
9	CTCF	chr6:44235563-44236375	HCT-116	colon:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
10	CTCF	chr6:44235628-44236292	K562	blood:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
11	RAD21	chr6:44235594-44236342	HCT-116	colon:	n/a	chr6:44235925-44235944 chr6:44235778-44235790
12	CTCF	chr6:44235675-44236184	HepG2	liver:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
13	CTCF	chr6:44235675-44236235	MCF-7	breast:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
14	RAD21	chr6:44235657-44236134	HepG2	liver:	n/a	chr6:44235925-44235944 chr6:44235778-44235790
15	CTCF	chr6:44235549-44236536	SK-N-SH	brain:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
16	CTCF	chr6:44235688-44236132	A549	lung:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
17	SMC3	chr6:44235580-44236925	SK-N-SH	brain:	n/a	n/a
18	CTCF	chr6:44235627-44236130	MCF-7	breast:	n/a	chr6:44235926-44235947 chr6:44235924-44235942
19	NFIC	chr6:44235640-44236150	ECC-1	luminal epithelium:	n/a	n/a
20	RAD21	chr6:44235564-44236390	HCT-116	colon:	n/a	chr6:44235925-44235944 chr6:44235778-44235790
21	TCF12	chr6:44235599-44236182	A549	lung:	n/a	chr6:44235876-44235883
22	GTF2F1	chr6:44235674-44236071	H1-hESC	embryonic stem cell:	n/a	n/a
23	RAD21	chr6:44235653-44236169	A549	lung:	n/a	chr6:44235925-44235944 chr6:44235778-44235790
24	CTCF	chr6:44235533-44236309	A549	lung:	n/a	chr6:44235926-44235947 chr6:44235924-44235942

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	chr6:44235516..44236382-chr6:44423771..44424641,3	K562	blood:
6	chr6:44234643..44237474-chr6:44296098..44297940,2	MCF-7	breast:
7	chr6:44235419..44235959-chr6:44307130..44307772,2	MCF-7	breast:
8	chr6:44233082..44237547-chr6:44353791..44357282,5	MCF-7	breast:
9	chr6:44235463..44235997-chr6:44306301..44306808,2	MCF-7	breast:
10	chr6:44234588..44237594-chr6:44277478..44280850,3	MCF-7	breast:
11	chr6:44084290..44087287-chr6:44233720..44236514,2	K562	blood:
12	chr6:44235214..44237013-chr6:44305028..44307078,2	MCF-7	breast:
13	chr6:44233695..44236268-chr6:44306586..44308563,3	K562	blood:
14	chr6:44235278..44236426-chr6:44305941..44306986,11	K562	blood:
15	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: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1283567	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs167772	0.84[CHD][hapmap]
rs2233437	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs324137	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs325000	0.81[JPT][hapmap]
rs325001	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs3799962	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3818685	0.80[CHD][hapmap]
rs483536	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]
rs498512	0.86[JPT][hapmap]
rs524533	0.82[ASW][hapmap];0.88[CEU][hapmap];0.81[TSI][hapmap]
rs545970	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs571770	0.82[ASW][hapmap];0.88[CEU][hapmap];0.81[TSI][hapmap]
rs639728	0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs651297	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs730775	0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.90[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs513688	HSP90AB1	cis	cerebellum	SCAN
rs513688	SLC22A7	cis	cerebellum	SCAN
rs513688	PLA2G7	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

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

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