Variant report

Variant	rs12097444
Chromosome Location	chr1:170504194-170504195
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:170500588-170509342	K562	blood:	n/a	n/a
2	POLR2A	chr1:170503772-170504285	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:170501854..170504832-chr1:170526241..170528551,2	MCF-7	breast:
2	chr1:170499494..170504219-chr1:170507198..170509728,4	K562	blood:
3	chr1:170499494..170507345-chr1:170507805..170517333,18	K562	blood:
4	chr1:170499484..170505100-chr1:170505427..170511134,13	MCF-7	breast:
5	chr1:170496299..170499124-chr1:170502580..170504696,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000231407	TF binding region
GORAB	TF binding region
ENSG00000120370	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10919427	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10919428	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12075840	0.86[AFR][1000 genomes]
rs2901402	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59597526	0.92[AFR][1000 genomes]
rs60696673	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6676293	0.86[AFR][1000 genomes]
rs73029152	0.81[AFR][1000 genomes]
rs73029169	1.00[AMR][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	nsv872543	chr1:170171083-170674903	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv533915	chr1:170258766-170725296	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170501800-170516000	Weak transcription	Spleen	Spleen
2	chr1:170502000-170506200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:170502000-170506200	Weak transcription	Gastric	stomach
4	chr1:170502000-170508400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:170502000-170515200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:170502000-170517200	Weak transcription	Esophagus	oesophagus
7	chr1:170502200-170508200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:170502200-170508400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:170502200-170508400	Weak transcription	Placenta	Placenta
10	chr1:170502200-170508400	Weak transcription	Fetal Thymus	thymus
11	chr1:170502200-170508400	Weak transcription	Thymus	Thymus
12	chr1:170502200-170521000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:170502400-170504200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:170502400-170506400	Weak transcription	Right Atrium	heart
15	chr1:170502400-170512200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:170502400-170514800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:170502600-170507200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:170502600-170507800	Weak transcription	Fetal Lung	lung
19	chr1:170502600-170508400	Weak transcription	Fetal Intestine Small	intestine
20	chr1:170502600-170508600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:170502600-170508600	Weak transcription	Fetal Brain Female	brain
22	chr1:170502600-170509000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:170502600-170509800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:170502600-170510200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:170502600-170510200	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:170502600-170511600	Weak transcription	Brain Substantia Nigra	brain
27	chr1:170502600-170512000	Weak transcription	Aorta	Aorta
28	chr1:170502600-170520800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:170502600-170523400	Weak transcription	Fetal Brain Male	brain
30	chr1:170502800-170504200	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr1:170502800-170504600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:170502800-170504800	Enhancers	HepG2	liver
33	chr1:170502800-170505400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:170502800-170506000	Weak transcription	Stomach Mucosa	stomach
35	chr1:170502800-170506400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:170502800-170506400	Weak transcription	Psoas Muscle	Psoas
37	chr1:170502800-170506400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:170502800-170506800	Weak transcription	A549	lung
39	chr1:170502800-170507200	Weak transcription	HUVEC	blood vessel
40	chr1:170502800-170507600	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr1:170502800-170507800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:170502800-170508200	Weak transcription	Fetal Stomach	stomach
43	chr1:170502800-170508400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:170502800-170508400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:170502800-170508400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:170502800-170508400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr1:170502800-170508400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:170502800-170508400	Weak transcription	Fetal Intestine Large	intestine
49	chr1:170502800-170508800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr1:170502800-170509600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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