Variant report

Variant	rs17346574
Chromosome Location	chr6:28697832-28697833
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr6:28697810-28698064	U2OS	brain:	n/a	n/a
2	KAP1	chr6:28696432-28698094	HEK293	kidney:	n/a	n/a
3	MYC	chr6:28696758-28698073	A549	lung:	n/a	n/a
4	ZNF384	chr6:28696910-28697943	K562	blood:	n/a	n/a
5	TEAD4	chr6:28696410-28697953	K562	blood:	n/a	n/a
6	MAX	chr6:28697742-28698281	A549	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28697819-28697869	AG09319	gingival:	n/a
2	chr6:28697819-28697869	LNCaP	prostate:	n/a
3	chr6:28697819-28697869	HEEpiC	esophagus:	n/a
4	chr6:28697819-28697869	K562	blood:	n/a
5	chr6:28697819-28697869	BE2_C	brain:	n/a
6	chr6:28697819-28697869	NB4	blood:	n/a
7	chr6:28697819-28697869	CMK	blood:	n/a
8	chr6:28697819-28697869	A549	lung:	n/a
9	chr6:28697819-28697869	HCM	heart:	n/a
10	chr6:28697819-28697869	GM12892	blood:	n/a
11	chr6:28697819-28697869	GM19239	blood:	n/a
12	chr6:28697819-28697869	RPTEC	kidney:	n/a
13	chr6:28697819-28697869	IMR90	lung:	fetal
14	chr6:28697819-28697869	ProgFib	skin:	n/a
15	chr6:28697819-28697869	GM06990	blood:	n/a
16	chr6:28697819-28697869	AG09309	skin:	n/a
17	chr6:28697819-28697869	Hela-S3	cervix:	n/a
18	chr6:28697819-28697869	SKMC	muscle:	n/a
19	chr6:28697819-28697869	SK-N-MC	brain:	n/a
20	chr6:28697819-28697869	AG04449	skin:	fetal
21	chr6:28697819-28697869	HNPCEpiC	eye:	n/a
22	chr6:28697819-28697869	ovcar-3	ovarian:	n/a
23	chr6:28697819-28697869	ECC-1	luminal epithelium:	n/a
24	chr6:28697819-28697869	AG10803	skin:	n/a
25	chr6:28697819-28697869	HMEC	breast:	n/a
26	chr6:28697819-28697869	Jurkat	blood:	n/a
27	chr6:28697819-28697869	T-47D	breast:	n/a
28	chr6:28697819-28697869	PANC-1	pancreas:	n/a
29	chr6:28697819-28697869	HCF	heart:	n/a
30	chr6:28697819-28697869	HUVEC	blood vessel:	n/a
31	chr6:28697819-28697869	HepG2	liver:	n/a
32	chr6:28697819-28697869	MCF-7	breast:	n/a
33	chr6:28697819-28697869	H1-hESC	embryonic stem cell:	embryo
34	chr6:28697819-28697869	NHDF-neo	bronchial:	n/a
35	chr6:28697819-28697869	HCPEpiC	choroid plexus:	n/a
36	chr6:28697819-28697869	AG04450	lung:	fetal
37	chr6:28697819-28697869	GM12891	blood:	n/a
38	chr6:28697819-28697869	HAEpiC	amniotic membrane:	n/a
39	chr6:28697819-28697869	SK-N-SH_RA	brain:	n/a
40	chr6:28697819-28697869	U87	brain:	n/a
41	chr6:28697819-28697869	GM12878	blood:	n/a
42	chr6:28697819-28697869	HRE	kidney:	n/a
43	chr6:28697819-28697869	SAEC	small airway:	n/a
44	chr6:28697819-28697869	NHBE	bronchial:	n/a
45	chr6:28697819-28697869	Hepatocyte	liver:	n/a
46	chr6:28697819-28697869	NT2-D1	testis:	n/a
47	chr6:28697819-28697869	Caco-2	colon:	n/a
48	chr6:28697819-28697869	HIPEpiC	eye:	n/a
49	chr6:28697819-28697869	NH-A	brain:	n/a
50	chr6:28697819-28697869	HL-60	blood:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr6:28695857..28698165-chr6:28761272..28763967,2	K562	blood:
2	chr6:28694465..28699409-chr6:28701823..28706376,12	K562	blood:
3	chr6:28666298..28671313-chr6:28695437..28699521,5	K562	blood:
4	chr6:28695842..28698712-chr6:28863478..28865661,2	K562	blood:
5	chr6:28695559..28699343-chr6:28721391..28727067,6	K562	blood:
6	chr6:28697655..28699447-chr6:28898332..28901038,2	K562	blood:
7	chr6:28695145..28698066-chr6:28723238..28727067,5	K562	blood:

No data

Variant related genes	Relation type
RPSAP2	TF binding region
RPSAP2	CpG island
ENSG00000265764	Chromatin interaction
ENSG00000224157	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10498733	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1233582	0.96[ASN][1000 genomes]
rs169682	0.94[AMR][1000 genomes]
rs17280797	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17280818	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17281186	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs185982	0.94[AMR][1000 genomes]
rs1936180	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209190	0.94[AMR][1000 genomes]
rs209192	0.94[AMR][1000 genomes]
rs209193	0.94[AMR][1000 genomes]
rs2754761	0.94[AMR][1000 genomes]
rs2754762	0.94[AMR][1000 genomes]
rs2754765	0.82[AMR][1000 genomes]
rs2765222	0.94[AMR][1000 genomes]
rs2765223	0.94[AMR][1000 genomes]
rs398795	0.94[AMR][1000 genomes]
rs453020	0.82[AMR][1000 genomes]
rs55659253	0.80[AMR][1000 genomes]
rs55764335	0.80[AMR][1000 genomes]
rs55891766	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56030816	0.83[AMR][1000 genomes]
rs56098960	0.80[AMR][1000 genomes]
rs56110474	0.82[AMR][1000 genomes]
rs56165011	0.80[AMR][1000 genomes]
rs56296645	0.82[AFR][1000 genomes]
rs56308612	0.94[AMR][1000 genomes]
rs56374518	0.94[AMR][1000 genomes]
rs56384403	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs57491524	0.88[AMR][1000 genomes]
rs57693980	0.82[AFR][1000 genomes]
rs57791058	0.80[AMR][1000 genomes]
rs57965355	0.80[AMR][1000 genomes]
rs58104924	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58238888	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs58258185	0.80[AMR][1000 genomes]
rs59959723	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60252686	0.80[AMR][1000 genomes]
rs60311527	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61094745	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61208746	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61703239	0.82[AFR][1000 genomes]
rs6909960	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6923795	0.80[AMR][1000 genomes]
rs6938988	0.88[AMR][1000 genomes]
rs6939948	0.82[AMR][1000 genomes]
rs7748319	0.92[ASN][1000 genomes]
rs7751451	0.80[AMR][1000 genomes]
rs7751884	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7755641	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7758798	0.80[AMR][1000 genomes]
rs7760656	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7765829	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7766599	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7772111	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7772682	0.84[ASN][1000 genomes]
rs9688414	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9767359	0.82[AFR][1000 genomes];0.80[AMR][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:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28695800-28698000	Active TSS	NH-A	brain
2	chr6:28695800-28698200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:28695800-28698200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr6:28696000-28698000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:28696000-28698000	Active TSS	HMEC	breast
6	chr6:28696200-28698000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:28696200-28698000	Active TSS	Ovary	ovary
8	chr6:28696200-28698400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr6:28696200-28698400	Active TSS	A549	lung
10	chr6:28696400-28698000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:28696400-28698000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:28696400-28698000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
13	chr6:28696400-28698000	Active TSS	Brain Hippocampus Middle	brain
14	chr6:28696400-28698000	Active TSS	NHDF-Ad	bronchial
15	chr6:28696400-28698200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:28696400-28698200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:28696400-28698200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:28696400-28698200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:28696400-28698200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:28696400-28698400	Active TSS	H9 Cell Line	embryonic stem cell
21	chr6:28696400-28698600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr6:28696600-28698000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr6:28696600-28698200	Active TSS	Right Atrium	heart
24	chr6:28696800-28698000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:28697000-28698000	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:28697200-28698000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:28697200-28698000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
28	chr6:28697200-28698200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:28697200-28698200	Active TSS	Adipose Nuclei	Adipose
30	chr6:28697200-28698400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
31	chr6:28697200-28698400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr6:28697400-28698000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
33	chr6:28697400-28698000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:28697600-28698000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:28697600-28698000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
36	chr6:28697600-28698000	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:28697600-28698000	Flanking Active TSS	NHEK	skin
38	chr6:28697600-28698000	Flanking Bivalent TSS/Enh	Osteobl	bone
39	chr6:28697800-28698000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:28697800-28698000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:28697800-28698000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:28697800-28698000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:28697800-28698000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:28697800-28698000	ZNF genes & repeats	Esophagus	oesophagus
45	chr6:28697800-28698000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
46	chr6:28697800-28698000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr6:28697800-28698000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
48	chr6:28697800-28698000	Flanking Active TSS	GM12878-XiMat	blood
49	chr6:28697800-28698000	Bivalent/Poised TSS	HepG2	liver
50	chr6:28697800-28698000	Flanking Active TSS	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links