Variant report

Variant	rs1233616
Chromosome Location	chr6:28739884-28739885
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

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	RAD21	chr6:28739409-28739913	H1-hESC	embryonic stem cell:	n/a	n/a
3	CREB1	chr6:28739433-28739884	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZBTB7A	chr6:28739819-28740036	K562	blood:	n/a	n/a
5	CBX3	chr6:28739360-28739915	K562	blood:	n/a	n/a
6	JUN	chr6:28738715-28741405	K562	blood:	n/a	n/a
7	MAZ	chr6:28739473-28739945	K562	blood:	n/a	n/a
8	CTCF	chr6:28739357-28739977	A549	lung:	n/a	n/a
9	CTCF	chr6:28739840-28739990	HEK293	kidney:	n/a	n/a
10	RAD21	chr6:28739290-28739917	HCT-116	colon:	n/a	n/a
11	SUZ12	chr6:28739658-28740034	H1-hESC	embryonic stem cell:	n/a	n/a
12	NR2F2	chr6:28739493-28740975	K562	blood:	n/a	n/a
13	ZNF263	chr6:28739514-28739985	HEK293-T-REx	kidney:	n/a	n/a
14	TCF7L2	chr6:28739799-28739968	Hela-S3	cervix:	n/a	n/a
15	CREB1	chr6:28739416-28739898	H1-hESC	embryonic stem cell:	n/a	n/a
16	ATF2	chr6:28739360-28739899	H1-hESC	embryonic stem cell:	n/a	n/a
17	RCOR1	chr6:28739465-28739901	K562	blood:	n/a	n/a
18	CTCF	chr6:28739800-28739950	HMEC	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28739783..28741376-chr6:28889070..28891885,2	MCF-7	breast:
2	chr6:28739105..28742072-chr6:28746732..28748309,2	K562	blood:
3	chr6:28739213..28740105-chr6:28777494..28778016,2	K562	blood:
4	chr4:150931384..150932353-chr6:28739643..28740217,2	K562	blood:
5	chr6:28739775..28742884-chr6:28756307..28759477,3	K562	blood:
6	chr6:28739291..28741599-chr6:28752490..28754377,2	K562	blood:
7	chr6:28715045..28717732-chr6:28737419..28740778,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000221191	TF binding region
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1233596	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1233601	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233602	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233603	0.85[ASN][1000 genomes]
rs1233605	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1233607	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1233615	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1233617	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	0.88[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	0.82[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

No data

Chromatin state (count:21 , 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	chr6:28738200-28740800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
3	chr6:28739200-28740600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:28739200-28740800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:28739400-28740000	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
6	chr6:28739400-28740000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:28739400-28740600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:28739600-28740000	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
9	chr6:28739600-28740000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
10	chr6:28739600-28740000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr6:28739600-28740200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
12	chr6:28739600-28740600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:28739600-28740800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:28739600-28741000	Flanking Active TSS	K562	blood
15	chr6:28739800-28740000	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:28739800-28740000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
17	chr6:28739800-28740000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:28739800-28740000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:28739800-28740000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr6:28739800-28740000	Active TSS	Hela-S3	cervix
21	chr6:28739800-28740200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links