Variant report

Variant	rs9472254
Chromosome Location	chr6:44306339-44306340
allele	C/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	NR2F2	chr6:44306129-44306729	K562	blood:	n/a	chr6:44306488-44306503
2	CTCF	chr6:44306315-44306579	Fibrobl	skin:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
3	CTCF	chr6:44306323-44306578	MCF-7	breast:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
4	RAD21	chr6:44305640-44306783	SK-N-SH	brain:	n/a	chr6:44306436-44306446 chr6:44306434-44306446 chr6:44306432-44306451 chr6:44306438-44306447 chr6:44306435-44306448
5	RAD21	chr6:44306211-44306568	GM12878	blood:	n/a	chr6:44306436-44306446 chr6:44306434-44306446 chr6:44306432-44306451 chr6:44306438-44306447 chr6:44306435-44306448
6	CTCF	chr6:44306320-44306470	NHEK	skin:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
7	CTCF	chr6:44306298-44306575	GM19239	blood:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
8	RAD21	chr6:44306195-44306663	GM12878	blood:	n/a	chr6:44306436-44306446 chr6:44306434-44306446 chr6:44306432-44306451 chr6:44306438-44306447 chr6:44306435-44306448
9	RAD21	chr6:44306179-44306669	H1-hESC	embryonic stem cell:	n/a	chr6:44306436-44306446 chr6:44306434-44306446 chr6:44306432-44306451 chr6:44306438-44306447 chr6:44306435-44306448
10	YY1	chr6:44306240-44306621	GM12878	blood:	n/a	n/a
11	ZNF143	chr6:44306238-44306623	GM12878	blood:	n/a	n/a
12	CTCF	chr6:44306318-44306577	LNCaP	prostate:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
13	SMC3	chr6:44306213-44306655	HepG2	liver:	n/a	chr6:44306436-44306450
14	CTCF	chr6:44306326-44306575	LNCaP	prostate:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
15	CTCF	chr6:44306205-44306627	ECC-1	luminal epithelium:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
16	CTCF	chr6:44306239-44306603	K562	blood:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
17	CTCF	chr6:44306288-44306615	H1-hESC	embryonic stem cell:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
18	RAD21	chr6:44306019-44306690	HCT-116	colon:	n/a	chr6:44306436-44306446 chr6:44306434-44306446 chr6:44306432-44306451 chr6:44306438-44306447 chr6:44306435-44306448
19	CTCF	chr6:44306223-44306644	IMR90	lung:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
20	CTCF	chr6:44306274-44306605	Spleen_OC	spleen:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
21	SMC3	chr6:44306160-44306867	K562	blood:	n/a	chr6:44306436-44306450
22	RCOR1	chr6:44306275-44306614	K562	blood:	n/a	n/a
23	RAD21	chr6:44306164-44306642	MCF-7	breast:	n/a	chr6:44306436-44306446 chr6:44306434-44306446 chr6:44306432-44306451 chr6:44306438-44306447 chr6:44306435-44306448
24	MAX	chr6:44306240-44306607	K562	blood:	n/a	n/a
25	CTCF	chr6:44306303-44306579	HepG2	liver:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
26	CTCF	chr6:44306019-44306808	HCT-116	colon:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
27	STAT1	chr6:44306336-44306538	GM12878	blood:	n/a	n/a
28	CTCF	chr6:44306300-44306605	GM19238	blood:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
29	CTCF	chr6:44306291-44306594	SK-N-SH_RA	brain:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
30	CTCF	chr6:44306040-44306902	A549	lung:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
31	SMC3	chr6:44306186-44306640	Hela-S3	cervix:	n/a	chr6:44306436-44306450
32	CTCF	chr6:44306305-44306573	Kidney_OC	kidney:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
33	CTCF	chr6:44306294-44306608	Medullo	brain:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
34	FOXM1	chr6:44306242-44306610	GM12878	blood:	n/a	n/a
35	CTCF	chr6:44306245-44306611	A549	lung:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
36	ZNF143	chr6:44306263-44306617	K562	blood:	n/a	n/a
37	MAZ	chr6:44306126-44306555	HepG2	liver:	n/a	n/a
38	RAD21	chr6:44306227-44306648	K562	blood:	n/a	chr6:44306436-44306446 chr6:44306434-44306446 chr6:44306432-44306451 chr6:44306438-44306447 chr6:44306435-44306448
39	RAD21	chr6:44306214-44306640	HepG2	liver:	n/a	chr6:44306436-44306446 chr6:44306434-44306446 chr6:44306432-44306451 chr6:44306438-44306447 chr6:44306435-44306448
40	RAD21	chr6:44306209-44306626	HepG2	liver:	n/a	chr6:44306436-44306446 chr6:44306434-44306446 chr6:44306432-44306451 chr6:44306438-44306447 chr6:44306435-44306448
41	ARID3A	chr6:44306275-44306548	HepG2	liver:	n/a	n/a
42	RAD21	chr6:44306137-44306754	A549	lung:	n/a	chr6:44306436-44306446 chr6:44306434-44306446 chr6:44306432-44306451 chr6:44306438-44306447 chr6:44306435-44306448
43	GTF2F1	chr6:44306273-44306584	H1-hESC	embryonic stem cell:	n/a	n/a
44	RAD21	chr6:44306264-44306622	GM12878	blood:	n/a	chr6:44306436-44306446 chr6:44306434-44306446 chr6:44306432-44306451 chr6:44306438-44306447 chr6:44306435-44306448
45	RAD21	chr6:44306095-44306647	Hela-S3	cervix:	n/a	chr6:44306436-44306446 chr6:44306434-44306446 chr6:44306432-44306451 chr6:44306438-44306447 chr6:44306435-44306448
46	CTCF	chr6:44306136-44306737	MCF-7	breast:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
47	CTCF	chr6:44306208-44306776	K562	blood:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452
48	MAX	chr6:44306292-44306612	NB4	blood:	n/a	n/a
49	JUND	chr6:44306276-44306616	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr6:44306302-44306593	K562	blood:	n/a	chr6:44306437-44306447 chr6:44306429-44306450 chr6:44306436-44306449 chr6:44306434-44306452

No.	Distal block	Cell Line	Cell type
1	chr6:44234120..44234767-chr6:44306292..44306910,2	MCF-7	breast:
2	chr6:44299856..44303347-chr6:44304768..44307907,5	K562	blood:
3	chr6:44235250..44236905-chr6:44304916..44306810,16	MCF-7	breast:
4	chr6:44231961..44235036-chr6:44304302..44308085,4	MCF-7	breast:
5	chr6:43742589..43743189-chr6:44305958..44306640,2	K562	blood:
6	chr6:44235278..44236426-chr6:44305941..44306986,11	K562	blood:
7	chr6:44295218..44297676-chr6:44304954..44307920,2	K562	blood:
8	chr6:44213371..44214265-chr6:44306195..44306927,2	MCF-7	breast:
9	chr6:44247321..44249117-chr6:44305925..44308606,2	K562	blood:
10	chr6:44235463..44235997-chr6:44306301..44306808,2	MCF-7	breast:
11	chr6:44235532..44236481-chr6:44305932..44306869,8	MCF-7	breast:
12	chr6:44064146..44065473-chr6:44305968..44306588,4	K562	blood:
13	chr6:44140104..44141091-chr6:44305973..44306927,4	K562	blood:
14	chr6:44279477..44281866-chr6:44305528..44307591,2	K562	blood:
15	chr6:44235214..44237013-chr6:44305028..44307078,2	MCF-7	breast:
16	chr6:43691294..43691819-chr6:44305809..44306480,2	K562	blood:
17	chr6:44119317..44120169-chr6:44306218..44306929,3	K562	blood:
18	chr6:44214075..44216789-chr6:44305650..44307657,3	MCF-7	breast:
19	chr6:44119482..44120143-chr6:44306003..44307071,3	MCF-7	breast:
20	chr6:44222748..44225647-chr6:44303433..44307988,6	K562	blood:

Variant related genes	Relation type
SPATS1	TF binding region
ENSG00000157593	Chromatin interaction
ENSG00000146232	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000124608	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12197830	0.91[AFR][1000 genomes]
rs1473563	0.91[AFR][1000 genomes]
rs1473564	0.91[AFR][1000 genomes]
rs1566528	0.85[YRI][hapmap]
rs1566529	0.85[YRI][hapmap]
rs2026309	0.82[YRI][hapmap];0.86[AFR][1000 genomes]
rs6931374	0.82[AFR][1000 genomes]
rs7747178	0.95[AFR][1000 genomes]
rs7763988	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7769324	0.85[YRI][hapmap]
rs9296429	0.86[AFR][1000 genomes]
rs994736	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44302600-44309600	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr6:44304000-44306800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:44305000-44306400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:44305000-44307400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:44305200-44307000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:44305200-44307400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:44305400-44310400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:44306000-44307600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr6:44306200-44306400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:44306200-44306400	Enhancers	Brain Substantia Nigra	brain
11	chr6:44306200-44306400	Enhancers	HMEC	breast
12	chr6:44306200-44306600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:44306200-44306800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr6:44306200-44309200	Weak transcription	Brain Germinal Matrix	brain

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