Variant report

Variant	rs9500949
Chromosome Location	chr6:29635181-29635182
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GTF2F1	chr6:29634822-29635242	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr6:29634582-29635379	H1-hESC	embryonic stem cell:	n/a	chr6:29635151-29635158
3	SIN3A	chr6:29634546-29635329	H1-hESC	embryonic stem cell:	n/a	n/a
4	NANOG	chr6:29634980-29635285	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:29634924-29635246	H1-hESC	embryonic stem cell:	n/a	n/a
6	TEAD4	chr6:29634981-29635395	H1-hESC	embryonic stem cell:	n/a	n/a
7	TEAD4	chr6:29634503-29635435	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr6:29634709-29635211	H1-hESC	embryonic stem cell:	n/a	n/a
9	TCF12	chr6:29634902-29635347	H1-hESC	embryonic stem cell:	n/a	chr6:29635161-29635171
10	TBP	chr6:29634326-29635443	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr6:29634146-29635632	H1-hESC	embryonic stem cell:	n/a	n/a
12	ATF2	chr6:29634911-29635326	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:29634949-29635237	H1-hESC	embryonic stem cell:	n/a	n/a
14	YY1	chr6:29634422-29635370	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr6:29634901-29635269	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr6:29634802-29635435	H1-hESC	embryonic stem cell:	n/a	n/a
17	ZNF143	chr6:29634893-29635325	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29635158-29635208	HEEpiC	esophagus:	n/a
2	chr6:29635158-29635208	MCF-7	breast:	n/a
3	chr6:29635158-29635208	PrEC	prostate:	n/a
4	chr6:29635158-29635208	PFSK-1	brain:	n/a
5	chr6:29635158-29635208	K562	blood:	n/a
6	chr6:29635158-29635208	HNPCEpiC	eye:	n/a
7	chr6:29635158-29635208	PANC-1	pancreas:	n/a
8	chr6:29635158-29635208	ProgFib	skin:	n/a
9	chr6:29635158-29635208	AG04449	skin:	fetal
10	chr6:29635158-29635208	HepG2	liver:	n/a
11	chr6:29635158-29635208	GM06990	blood:	n/a
12	chr6:29635158-29635208	ovcar-3	ovarian:	n/a
13	chr6:29635158-29635208	SK-N-SH	brain:	n/a
14	chr6:29635158-29635208	AG09319	gingival:	n/a
15	chr6:29635158-29635208	NT2-D1	testis:	n/a
16	chr6:29635158-29635208	AG04450	lung:	fetal
17	chr6:29635158-29635208	BE2_C	brain:	n/a
18	chr6:29635158-29635208	HL-60	blood:	n/a
19	chr6:29635158-29635208	NHDF-neo	bronchial:	n/a
20	chr6:29635158-29635208	HPAEpiC	pulmonary alveolar:	n/a
21	chr6:29635158-29635208	A549	lung:	n/a
22	chr6:29635158-29635208	SK-N-MC	brain:	n/a
23	chr6:29635158-29635208	HCT-116	colon:	n/a
24	chr6:29635158-29635208	SK-N-SH_RA	brain:	n/a
25	chr6:29635158-29635208	HRCEpiC	kidney:	n/a
26	chr6:29635158-29635208	MCF10A-Er-Src	breast:	n/a
27	chr6:29635158-29635208	HMEC	breast:	n/a
28	chr6:29635158-29635208	HAEpiC	amniotic membrane:	n/a
29	chr6:29635158-29635208	AG10803	skin:	n/a
30	chr6:29635158-29635208	Hepatocyte	liver:	n/a
31	chr6:29635158-29635208	GM12891	blood:	n/a
32	chr6:29635158-29635208	AG09309	skin:	n/a
33	chr6:29635158-29635208	HEK293	kidney:	embryo
34	chr6:29635158-29635208	LNCaP	prostate:	n/a
35	chr6:29635158-29635208	NHBE	bronchial:	n/a
36	chr6:29635158-29635208	BJ	skin:	n/a
37	chr6:29635158-29635208	HCPEpiC	choroid plexus:	n/a
38	chr6:29635158-29635208	HIPEpiC	eye:	n/a
39	chr6:29635158-29635208	HCF	heart:	n/a
40	chr6:29635158-29635208	RPTEC	kidney:	n/a
41	chr6:29635158-29635208	GM19239	blood:	n/a
42	chr6:29635158-29635208	CMK	blood:	n/a
43	chr6:29635158-29635208	HRPEpiC	eye:	n/a
44	chr6:29635158-29635208	Jurkat	blood:	n/a
45	chr6:29635158-29635208	T-47D	breast:	n/a
46	chr6:29635158-29635208	H1-hESC	embryonic stem cell:	embryo
47	chr6:29635158-29635208	HCM	heart:	n/a
48	chr6:29635158-29635208	SAEC	small airway:	n/a
49	chr6:29635158-29635208	GM12892	blood:	n/a
50	chr6:29635158-29635208	ECC-1	luminal epithelium:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29634001..29636635-chr6:29639490..29642126,2	K562	blood:

No data

Variant related genes	Relation type
MOG	TF binding region
MOG	CpG island

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs17178077	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9295809	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468565	0.94[AFR][1000 genomes]
rs9468566	0.94[AFR][1000 genomes]
rs9468569	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468578	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468581	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9468590	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9500950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9500951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9500952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9500953	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9500954	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9500959	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9501680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29630800-29643200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:29631400-29640200	Weak transcription	NHEK	skin
4	chr6:29631800-29635200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:29632000-29636200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:29632000-29638600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:29633400-29635200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:29633400-29635600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:29633400-29635600	Genic enhancers	Brain Substantia Nigra	brain
10	chr6:29633400-29636000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr6:29633400-29636400	Enhancers	Fetal Heart	heart
12	chr6:29633600-29635400	Genic enhancers	Brain Hippocampus Middle	brain
13	chr6:29633600-29636600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:29633800-29635800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:29633800-29636600	Enhancers	H9 Cell Line	embryonic stem cell
16	chr6:29634000-29636200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:29634200-29635400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:29634400-29635600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr6:29634400-29635800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr6:29634400-29636200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:29634600-29635200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr6:29634600-29635400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:29634600-29635600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr6:29634600-29636400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:29634600-29641000	Weak transcription	Brain Anterior Caudate	brain
26	chr6:29634600-29642000	Weak transcription	Brain Angular Gyrus	brain
27	chr6:29634800-29635200	Enhancers	HSMMtube	muscle
28	chr6:29634800-29636200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr6:29635000-29635200	Genic enhancers	Brain Inferior Temporal Lobe	brain
30	chr6:29635000-29635200	Bivalent Enhancer	HepG2	liver
31	chr6:29635000-29635400	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr6:29635000-29635400	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr6:29635000-29635600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:29635000-29636000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr6:29635000-29636400	Enhancers	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links