Variant report

Variant	rs6788474
Chromosome Location	chr3:119218903-119218904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:119218599-119218931	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:119218368-119219001	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:119218321-119220778	K562	blood:	n/a	n/a
4	MYC	chr3:119218461-119219000	K562	blood:	n/a	n/a
5	MXI1	chr3:119216044-119220289	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr3:119218751-119218946	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr3:119218817-119218956	K562	blood:	n/a	n/a
8	STAT3	chr3:119218854-119218992	MCF10A-Er-Src	breast:	n/a	n/a
9	TBL1XR1	chr3:119218801-119218949	K562	blood:	n/a	n/a
10	POLR2A	chr3:119215979-119219829	SK-N-MC	brain:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119218133..119220642-chr3:119277892..119280066,2	K562	blood:
2	chr3:119182024..119184224-chr3:119215586..119219856,7	MCF-7	breast:
3	chr3:119185641..119191138-chr3:119214841..119219392,9	MCF-7	breast:
4	chr3:119186169..119189555-chr3:119214375..119219589,12	K562	blood:
5	chr3:119215976..119218932-chr3:119393949..119396539,3	K562	blood:
6	chr3:119186243..119189555-chr3:119215703..119218960,7	K562	blood:
7	chr3:119185037..119191105-chr3:119214944..119221331,23	MCF-7	breast:
8	chr3:119217361..119219124-chr3:119394788..119396855,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272662	TF binding region
TIMMDC1	TF binding region
ENSG00000138495	Chromatin interaction
ENSG00000163389	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000121594	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11707612	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11709468	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714738	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11714843	0.92[ASN][1000 genomes]
rs11719448	0.91[ASN][1000 genomes]
rs11720158	0.91[ASN][1000 genomes]
rs11720423	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1599795	0.91[ASN][1000 genomes]
rs1599796	0.91[ASN][1000 genomes]
rs17203188	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1938	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1961132	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2049500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276713	0.91[ASN][1000 genomes]
rs2280670	0.93[ASN][1000 genomes]
rs2293371	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34090996	0.87[ASN][1000 genomes]
rs3732418	0.91[ASN][1000 genomes]
rs3755579	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4447803	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4461452	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688009	0.93[ASN][1000 genomes]
rs4688011	0.91[ASN][1000 genomes]
rs4688013	0.91[ASN][1000 genomes]
rs57506457	0.86[ASN][1000 genomes]
rs59024323	0.93[ASN][1000 genomes]
rs60938951	0.83[ASN][1000 genomes]
rs62263444	0.89[ASN][1000 genomes]
rs62264483	0.91[ASN][1000 genomes]
rs62264487	0.91[ASN][1000 genomes]
rs6438534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610335	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9289131	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9832341	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9850413	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869760	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6788474	KTELC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119216200-119219200	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr3:119216200-119219600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr3:119216200-119219600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr3:119216200-119219800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:119216200-119220000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:119216400-119219200	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr3:119216400-119219400	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr3:119216400-119219600	Active TSS	Psoas Muscle	Psoas
9	chr3:119216400-119220200	Active TSS	K562	blood
10	chr3:119216600-119219000	Active TSS	H9 Cell Line	embryonic stem cell
11	chr3:119216600-119219800	Active TSS	Left Ventricle	heart
12	chr3:119217600-119219000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:119218000-119219000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:119218000-119219000	Enhancers	Stomach Mucosa	stomach
15	chr3:119218000-119219200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:119218000-119220400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr3:119218000-119224400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:119218000-119225000	Weak transcription	Gastric	stomach
19	chr3:119218000-119231800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:119218000-119236600	Weak transcription	Aorta	Aorta
21	chr3:119218200-119219000	Enhancers	Primary B cells from cord blood	blood
22	chr3:119218200-119219000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr3:119218200-119219000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr3:119218200-119219000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:119218200-119219000	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr3:119218200-119219000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr3:119218200-119219000	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr3:119218200-119219000	Flanking Active TSS	NH-A	brain
29	chr3:119218200-119219200	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr3:119218200-119219200	Weak transcription	Ovary	ovary
31	chr3:119218200-119219400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:119218200-119219400	Enhancers	Primary hematopoietic stem cells	blood
33	chr3:119218200-119219400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:119218200-119219400	Flanking Active TSS	HepG2	liver
35	chr3:119218200-119219400	Flanking Active TSS	NHEK	skin
36	chr3:119218200-119219600	Flanking Active TSS	Dnd41	blood
37	chr3:119218200-119219800	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr3:119218200-119219800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:119218200-119219800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:119218200-119220000	Enhancers	Primary B cells from peripheral blood	blood
41	chr3:119218200-119220000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:119218200-119220000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr3:119218200-119220000	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr3:119218200-119220800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:119218400-119219000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:119218400-119219000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:119218400-119219000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr3:119218400-119219000	Genic enhancers	Fetal Muscle Trunk	muscle
49	chr3:119218400-119219000	Enhancers	Fetal Muscle Leg	muscle
50	chr3:119218400-119219000	Flanking Active TSS	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links