Variant report

Variant	rs3790444
Chromosome Location	chr1:93304190-93304191
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:93303001-93304270	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:93304070-93304399	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:93303931-93304696	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:93304072-93304333	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:93304008-93304450	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr1:93303954-93304443	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:93301729-93304411	K562	blood:	n/a	n/a
8	POLR2A	chr1:93303974-93304463	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:93303926-93304375	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:93301994-93304325	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:93303955-93304467	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:93303274-93305956	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:93301951-93304524	HepG2	liver:	n/a	n/a
14	POLR2A	chr1:93302592-93304325	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:93301434-93307185	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr1:93303363-93304272	K562	blood:	n/a	n/a
17	POLR2A	chr1:93304028-93304392	K562	blood:	n/a	n/a
18	POLR2A	chr1:93304071-93304235	Hela-S3	cervix:	n/a	n/a
19	NFE2	chr1:93304127-93304318	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:93304149-93304444	HepG2	liver:	n/a	n/a
21	POLR2A	chr1:93301402-93304643	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr1:93303348-93304208	A549	lung:	n/a	n/a
23	POLR2A	chr1:93304103-93304496	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr1:93303980-93304322	K562	blood:	n/a	n/a
25	POLR2A	chr1:93303166-93307156	K562	blood:	n/a	n/a
26	POLR2A	chr1:93304004-93304436	GM12892	blood:	n/a	n/a
27	POLR2A	chr1:93301952-93304401	GM12891	blood:	n/a	n/a
28	POLR2A	chr1:93301216-93310285	K562	blood:	n/a	n/a
29	POLR2A	chr1:93303956-93304463	K562	blood:	n/a	n/a
30	POLR2A	chr1:93301817-93304585	HepG2	liver:	n/a	n/a
31	POLR2A	chr1:93303264-93304423	SK-N-MC	brain:	n/a	n/a
32	POLR2A	chr1:93304161-93304286	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:93302921..93305469-chr1:93643662..93645581,2	K562	blood:
2	chr1:93251020..93253744-chr1:93303793..93305482,2	K562	blood:
3	chr1:93214862..93218519-chr1:93302722..93305780,4	K562	blood:
4	chr1:93303345..93305385-chr1:93311213..93313203,2	MCF-7	breast:

No data

Variant related genes	Relation type
SNORA66	TF binding region
ENSG00000207022	Chromatin interaction
ENSG00000122483	Chromatin interaction
ENSG00000234202	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10218670	1.00[JPT][hapmap]
rs10735782	1.00[JPT][hapmap]
rs10735783	1.00[JPT][hapmap]
rs10747448	1.00[JPT][hapmap]
rs10747449	1.00[JPT][hapmap]
rs10747450	1.00[JPT][hapmap]
rs10782940	1.00[JPT][hapmap]
rs10874729	1.00[JPT][hapmap]
rs10874731	1.00[JPT][hapmap]
rs11164804	1.00[JPT][hapmap]
rs11164808	1.00[JPT][hapmap]
rs11164813	1.00[JPT][hapmap]
rs11164845	1.00[JPT][hapmap]
rs1337109	1.00[JPT][hapmap]
rs1415294	1.00[JPT][hapmap]
rs1415295	1.00[JPT][hapmap]
rs1538029	1.00[JPT][hapmap]
rs1932966	1.00[JPT][hapmap]
rs2065916	1.00[JPT][hapmap]
rs2107520	1.00[JPT][hapmap]
rs2107521	1.00[JPT][hapmap]
rs2158446	1.00[JPT][hapmap]
rs2244496	1.00[JPT][hapmap]
rs2391196	1.00[JPT][hapmap]
rs2391199	1.00[JPT][hapmap]
rs2391200	1.00[JPT][hapmap]
rs2774941	1.00[JPT][hapmap]
rs2774947	1.00[JPT][hapmap]
rs2811599	1.00[JPT][hapmap]
rs35054144	1.00[JPT][hapmap]
rs3790445	1.00[JPT][hapmap]
rs3790446	1.00[JPT][hapmap]
rs4847247	1.00[JPT][hapmap]
rs4847266	1.00[JPT][hapmap]
rs4847363	1.00[JPT][hapmap]
rs4847370	1.00[JPT][hapmap]
rs6604003	1.00[JPT][hapmap]
rs6604010	1.00[JPT][hapmap]
rs6604015	1.00[JPT][hapmap]
rs6604018	1.00[JPT][hapmap]
rs6661600	1.00[JPT][hapmap]
rs6671421	1.00[JPT][hapmap]
rs6685705	1.00[JPT][hapmap]
rs6696636	1.00[JPT][hapmap]
rs6703467	1.00[JPT][hapmap]
rs7416169	1.00[JPT][hapmap]
rs7513815	1.00[JPT][hapmap]
rs7516141	1.00[JPT][hapmap]
rs7526582	1.00[JPT][hapmap]
rs7529332	1.00[JPT][hapmap]
rs7529630	1.00[JPT][hapmap]
rs7540407	1.00[JPT][hapmap]
rs7543327	1.00[JPT][hapmap]
rs7543964	1.00[JPT][hapmap]
rs7549844	1.00[JPT][hapmap]
rs927339	1.00[JPT][hapmap]
rs932637	1.00[JPT][hapmap]
rs9439920	1.00[JPT][hapmap]
rs945724	1.00[JPT][hapmap]
rs976208	1.00[JPT][hapmap]

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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv530047	chr1:93273425-93308213	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv508393	chr1:93290513-93344924	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 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	chr1:93299200-93305400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
2	chr1:93299200-93306200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:93299200-93310400	Strong transcription	Fetal Muscle Trunk	muscle
4	chr1:93299400-93307200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:93299400-93309200	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr1:93299600-93304400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr1:93299600-93306000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:93299600-93306600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr1:93299600-93309000	Weak transcription	Esophagus	oesophagus
10	chr1:93299600-93309800	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:93299600-93310000	Strong transcription	Placenta	Placenta
12	chr1:93299600-93310400	Strong transcription	Fetal Thymus	thymus
13	chr1:93299800-93304200	Weak transcription	Gastric	stomach
14	chr1:93299800-93304400	Genic enhancers	NHDF-Ad	bronchial
15	chr1:93299800-93310600	Strong transcription	Fetal Intestine Large	intestine
16	chr1:93299800-93311600	Strong transcription	Fetal Muscle Leg	muscle
17	chr1:93300000-93305000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:93300000-93305800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr1:93300000-93306000	Genic enhancers	Primary T cells from cord blood	blood
20	chr1:93300000-93306200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:93300000-93309800	Strong transcription	Thymus	Thymus
22	chr1:93300000-93310000	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:93300000-93310000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:93300000-93310200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:93300200-93305400	Genic enhancers	HepG2	liver
26	chr1:93300200-93306000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr1:93300200-93306000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:93300200-93306600	Strong transcription	Fetal Kidney	kidney
29	chr1:93300200-93308000	Strong transcription	Colonic Mucosa	Colon
30	chr1:93300200-93309200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:93300200-93310000	Strong transcription	HSMMtube	muscle
32	chr1:93300200-93310200	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr1:93300200-93310400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:93300400-93305000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:93300400-93305000	Strong transcription	Fetal Lung	lung
36	chr1:93300400-93305800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:93300400-93306600	Strong transcription	Lung	lung
38	chr1:93300400-93310000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:93300400-93316000	Strong transcription	Primary B cells from cord blood	blood
40	chr1:93300600-93304200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:93300600-93304400	Genic enhancers	Osteobl	bone
42	chr1:93300600-93305200	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr1:93300600-93308800	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr1:93300600-93309200	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:93300600-93310000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:93300800-93304400	Genic enhancers	NHEK	skin
47	chr1:93300800-93304800	Weak transcription	Ovary	ovary
48	chr1:93300800-93304800	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:93300800-93305600	Weak transcription	Fetal Brain Male	brain
50	chr1:93300800-93306200	Genic enhancers	Duodenum Mucosa	Duodenum

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