Variant report

Variant	rs1233615
Chromosome Location	chr6:28739584-28739585
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:113)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:113 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr6:28739377-28739936	HEK293	kidney:	n/a	n/a
2	CTCF	chr6:28739500-28739650	NHEK	skin:	n/a	n/a
3	CTCF	chr6:28739540-28739690	GM12864	blood:	n/a	n/a
4	BACH1	chr6:28739412-28739709	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr6:28739560-28739710	WERI-Rb-1	eye:	n/a	n/a
6	CTCF	chr6:28739425-28739752	MCF-7	breast:	n/a	n/a
7	RAD21	chr6:28739409-28739913	H1-hESC	embryonic stem cell:	n/a	n/a
8	FOS	chr6:28739214-28739587	MCF10A-Er-Src	breast:	n/a	n/a
9	CTCF	chr6:28739520-28739670	Caco-2	colon:	n/a	n/a
10	RAD21	chr6:28739400-28739759	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr6:28739580-28739730	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr6:28739500-28739650	GM12870	blood:	n/a	n/a
13	CTCF	chr6:28739555-28739731	GM12878	blood:	n/a	n/a
14	CREB1	chr6:28739433-28739884	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAFK	chr6:28739539-28739739	H1-hESC	embryonic stem cell:	n/a	n/a
16	ZNF384	chr6:28739497-28739787	K562	blood:	n/a	n/a
17	CTCF	chr6:28739500-28739650	GM12878	blood:	n/a	n/a
18	CTCF	chr6:28739500-28739650	GM12872	blood:	n/a	n/a
19	CTCF	chr6:28739500-28739650	GM12873	blood:	n/a	n/a
20	UBTF	chr6:28739539-28739757	K562	blood:	n/a	n/a
21	CTCF	chr6:28739559-28739704	MCF-7	breast:	n/a	n/a
22	CTCF	chr6:28739400-28739690	SAEC	small airway:	n/a	n/a
23	CTCF	chr6:28739560-28739710	MCF-7	breast:	n/a	n/a
24	CTCF	chr6:28739580-28739730	MCF-7	breast:	n/a	n/a
25	RAD21	chr6:28739534-28739755	K562	blood:	n/a	n/a
26	CTCF	chr6:28739570-28739699	HepG2	liver:	n/a	n/a
27	CTCF	chr6:28739520-28739670	GM12867	blood:	n/a	n/a
28	CTCF	chr6:28739557-28739735	NHEK	skin:	n/a	n/a
29	CTCF	chr6:28739520-28739670	HL-60	blood:	n/a	n/a
30	ZNF143	chr6:28739470-28739809	K562	blood:	n/a	n/a
31	CBX3	chr6:28739360-28739915	K562	blood:	n/a	n/a
32	CTCF	chr6:28739501-28739714	A549	lung:	n/a	n/a
33	JUN	chr6:28738715-28741405	K562	blood:	n/a	n/a
34	CTCF	chr6:28739560-28739710	BE2_C	brain:	n/a	n/a
35	CTCF	chr6:28739540-28739690	HRPEpiC	eye:	n/a	n/a
36	CTCF	chr6:28739480-28739630	HCM	heart:	n/a	n/a
37	TBL1XR1	chr6:28739473-28739725	K562	blood:	n/a	n/a
38	FOS	chr6:28739224-28739585	MCF10A-Er-Src	breast:	n/a	n/a
39	CTCF	chr6:28739560-28739710	GM12872	blood:	n/a	n/a
40	CTCF	chr6:28739560-28739710	GM12874	blood:	n/a	n/a
41	CTCF	chr6:28739580-28739730	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr6:28739500-28739650	GM12874	blood:	n/a	n/a
43	CTCF	chr6:28739582-28739705	MCF-7	breast:	n/a	n/a
44	CTCF	chr6:28739566-28739732	A549	lung:	n/a	n/a
45	MAZ	chr6:28739473-28739945	K562	blood:	n/a	n/a
46	BACH1	chr6:28739377-28739604	K562	blood:	n/a	n/a
47	MYC	chr6:28739540-28739740	K562	blood:	n/a	n/a
48	RAD21	chr6:28739471-28739827	K562	blood:	n/a	n/a
49	ATF2	chr6:28739424-28739844	H1-hESC	embryonic stem cell:	n/a	n/a
50	RAD21	chr6:28739507-28739719	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28739105..28742072-chr6:28746732..28748309,2	K562	blood:
2	chr6:28739213..28740105-chr6:28777494..28778016,2	K562	blood:
3	chr6:28739291..28741599-chr6:28752490..28754377,2	K562	blood:
4	chr6:28737910..28739642-chr6:28829627..28831368,2	K562	blood:
5	chr6:28715045..28717732-chr6:28737419..28740778,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000221191	TF binding region
ENSG00000225595	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1002925	0.81[EUR][1000 genomes]
rs1233572	0.81[EUR][1000 genomes]
rs1233575	0.81[EUR][1000 genomes]
rs1233576	0.83[EUR][1000 genomes]
rs1233584	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1233596	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1233601	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233602	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233603	0.86[ASN][1000 genomes]
rs1233605	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1233607	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233616	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1233617	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1235176	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1539585	0.84[EUR][1000 genomes]
rs169683	0.83[EUR][1000 genomes]
rs1742742	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs209164	0.82[EUR][1000 genomes]
rs209171	0.83[EUR][1000 genomes]
rs209173	0.84[EUR][1000 genomes]
rs209176	0.81[EUR][1000 genomes]
rs209179	0.84[EUR][1000 genomes]
rs209184	0.83[EUR][1000 genomes]
rs209186	0.82[EUR][1000 genomes]
rs2208536	0.83[EUR][1000 genomes]
rs2754764	0.83[EUR][1000 genomes]
rs2754767	0.83[EUR][1000 genomes]
rs2765218	0.82[EUR][1000 genomes]
rs2765219	0.83[EUR][1000 genomes]
rs3131342	0.83[EUR][1000 genomes]
rs3132371	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3132386	0.81[EUR][1000 genomes]
rs377392	0.83[EUR][1000 genomes]
rs386628	0.83[EUR][1000 genomes]
rs393431	0.81[EUR][1000 genomes]
rs526983	0.84[EUR][1000 genomes]
rs7772289	0.82[EUR][1000 genomes]
rs9257134	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9257135	0.84[EUR][1000 genomes];0.86[ASN][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	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1233615	HIST1H2BH	cis	cerebellum	SCAN
rs1233615	ZSCAN23	cis	cerebellum	SCAN
rs1233615	ZNF323	cis	parietal	SCAN
rs1233615	ZKSCAN3	cis	cerebellum	SCAN
rs1233615	ZSCAN16	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28733600-28740800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:28737200-28739600	Enhancers	K562	blood
3	chr6:28738200-28740800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
4	chr6:28738400-28739600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
5	chr6:28738400-28739600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
6	chr6:28739200-28739600	Bivalent Enhancer	HMEC	breast
7	chr6:28739200-28740600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:28739200-28740800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:28739400-28739600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
10	chr6:28739400-28739800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:28739400-28740000	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
12	chr6:28739400-28740000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:28739400-28740600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell

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