Variant report

Variant	rs11679685
Chromosome Location	chr2:48669164-48669165
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr2:48666327-48669474	SK-N-SH	brain:	n/a	chr2:48667567-48667582 chr2:48668199-48668214 chr2:48667569-48667584
2	POLR2A	chr2:48666592-48669629	IMR90	lung:	n/a	n/a
3	POLR2A	chr2:48667332-48669765	GM12878	blood:	n/a	n/a
4	JUN	chr2:48666584-48669380	K562	blood:	n/a	chr2:48667757-48667768
5	POLR2A	chr2:48667010-48669236	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr2:48667222-48671944	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:48666828..48669731-chr2:48691807..48694698,2	MCF-7	breast:
2	chr2:48009081..48011260-chr2:48666512..48669305,2	K562	blood:
3	chr17:62500259..62503119-chr2:48667200..48670117,2	MCF-7	breast:
4	chr2:48009330..48011315-chr2:48667151..48669363,2	MCF-7	breast:
5	chr2:48668357..48671385-chr2:48673634..48677025,4	K562	blood:
6	chr2:48132531..48135272-chr2:48667743..48670607,2	K562	blood:
7	chr2:48540677..48543829-chr2:48665802..48669252,3	K562	blood:
8	chr2:47401201..47404315-chr2:48668410..48671549,3	K562	blood:
9	chr2:48131056..48133889-chr2:48666649..48669305,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272663	TF binding region
ENSG00000162869	Chromatin interaction
ENSG00000170802	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000116062	Chromatin interaction
ENSG00000258890	Chromatin interaction
ENSG00000233230	Chromatin interaction
ENSG00000138081	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10182093	0.83[EUR][1000 genomes]
rs10191938	0.83[EUR][1000 genomes]
rs10195717	0.84[EUR][1000 genomes]
rs10197359	0.84[EUR][1000 genomes]
rs11674217	0.91[EUR][1000 genomes]
rs11675947	0.91[AMR][1000 genomes]
rs11676078	0.91[EUR][1000 genomes]
rs11678825	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11678934	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11680968	0.81[EUR][1000 genomes]
rs11682838	0.90[EUR][1000 genomes]
rs11683202	0.91[EUR][1000 genomes]
rs11687276	0.81[EUR][1000 genomes]
rs11687461	0.82[EUR][1000 genomes]
rs11687498	0.80[AMR][1000 genomes]
rs11687771	0.87[AMR][1000 genomes]
rs11687851	0.83[EUR][1000 genomes]
rs11689288	0.80[AMR][1000 genomes]
rs11690526	0.87[AMR][1000 genomes]
rs11691302	0.91[EUR][1000 genomes]
rs11691407	0.91[EUR][1000 genomes]
rs11692537	0.91[EUR][1000 genomes]
rs11693784	0.87[AMR][1000 genomes]
rs11694094	0.91[EUR][1000 genomes]
rs11694955	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13398456	0.84[EUR][1000 genomes]
rs17397449	0.93[EUR][1000 genomes]
rs28505584	0.91[EUR][1000 genomes]
rs2937	0.87[AMR][1000 genomes]
rs4364065	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72889641	0.84[EUR][1000 genomes]
rs7573281	0.91[EUR][1000 genomes]
rs7584796	0.91[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	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11679685	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48667000-48669200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr2:48667000-48669200	Active TSS	Brain Anterior Caudate	brain
3	chr2:48667000-48669200	Active TSS	Stomach Smooth Muscle	stomach
4	chr2:48667000-48669400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:48667000-48669400	Active TSS	NHDF-Ad	bronchial
6	chr2:48667000-48669400	Active TSS	NHLF	lung
7	chr2:48667200-48669200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr2:48667200-48669200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr2:48668200-48669200	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr2:48668200-48669200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:48668200-48669200	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr2:48668200-48669400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:48668200-48669600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr2:48668200-48669600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:48668400-48669200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:48668400-48669200	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr2:48668400-48669200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr2:48668400-48669200	Flanking Active TSS	Fetal Brain Female	brain
19	chr2:48668400-48669200	Flanking Active TSS	K562	blood
20	chr2:48668400-48669400	Flanking Active TSS	Dnd41	blood
21	chr2:48668400-48669600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr2:48668600-48669200	Flanking Active TSS	A549	lung
23	chr2:48668600-48669200	Flanking Active TSS	NHEK	skin
24	chr2:48668600-48669400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:48668600-48669400	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr2:48668600-48669400	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr2:48668600-48682000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:48668800-48669200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr2:48668800-48669200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr2:48668800-48669200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:48668800-48669200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:48668800-48669200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr2:48668800-48669200	Active TSS	Brain Cingulate Gyrus	brain
34	chr2:48668800-48669200	Flanking Bivalent TSS/Enh	HepG2	liver
35	chr2:48668800-48669400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:48668800-48669400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr2:48668800-48669400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:48668800-48669400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr2:48668800-48669400	Active TSS	Osteobl	bone
40	chr2:48668800-48669600	Enhancers	Fetal Brain Male	brain
41	chr2:48668800-48669600	Enhancers	Stomach Mucosa	stomach
42	chr2:48668800-48669800	Weak transcription	Spleen	Spleen
43	chr2:48668800-48670200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr2:48668800-48670400	Weak transcription	Gastric	stomach
45	chr2:48668800-48671200	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr2:48668800-48671600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr2:48668800-48672200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr2:48668800-48672600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:48668800-48672600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr2:48668800-48672600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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