Variant report

Variant	rs1367615
Chromosome Location	chr3:88112584-88112585
allele	C/T
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	POLR2A	chr3:88112270-88113705	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:88111449..88113297-chr3:88120532..88122822,2	K562	blood:
2	chr3:88105473..88111150-chr3:88112060..88119652,14	K562	blood:
3	chr3:88111449..88113994-chr3:88120532..88124879,4	K562	blood:
4	chr3:88106854..88110640-chr3:88110801..88115329,7	K562	blood:

Variant related genes	Relation type
CGGBP1	TF binding region
ENSG00000229729	Chromatin interaction
ENSG00000163320	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11128023	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1431154	1.00[EUR][1000 genomes]
rs1594453	1.00[EUR][1000 genomes]
rs1594455	1.00[EUR][1000 genomes]
rs1604700	1.00[EUR][1000 genomes]
rs1897238	1.00[EUR][1000 genomes]
rs2033390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2567037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2735557	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241549	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241550	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4287925	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4404474	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4425287	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4443201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4513473	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4515075	1.00[EUR][1000 genomes]
rs4616669	1.00[EUR][1000 genomes]
rs4858927	1.00[EUR][1000 genomes]
rs4858933	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4858970	1.00[EUR][1000 genomes]
rs4858987	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4858988	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4858989	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7615309	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7621357	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7625641	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7633215	0.88[ASN][1000 genomes]
rs7633486	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7636845	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7650749	1.00[EUR][1000 genomes]
rs7650912	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7650915	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs930154	1.00[EUR][1000 genomes]
rs9310062	1.00[EUR][1000 genomes]
rs9310063	1.00[EUR][1000 genomes]
rs9310064	0.84[AFR][1000 genomes]
rs9310069	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812903	1.00[EUR][1000 genomes]
rs9833231	1.00[EUR][1000 genomes]
rs9850550	1.00[EUR][1000 genomes]
rs9860113	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9864564	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867614	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	nsv877146	chr3:87983962-88159835	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88109400-88115000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:88109400-88115000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:88109400-88115400	Weak transcription	Lung	lung
4	chr3:88109400-88124400	Weak transcription	Pancreas	Pancrea
5	chr3:88109600-88113000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:88109800-88112800	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr3:88109800-88113000	Weak transcription	Left Ventricle	heart
8	chr3:88109800-88113000	Weak transcription	Ovary	ovary
9	chr3:88109800-88113600	Weak transcription	Placenta	Placenta
10	chr3:88109800-88113800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr3:88109800-88113800	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr3:88109800-88115000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr3:88109800-88115400	Weak transcription	Fetal Intestine Small	intestine
14	chr3:88110000-88113200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:88110000-88113400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:88110000-88116600	Weak transcription	Thymus	Thymus
17	chr3:88110000-88118600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:88110000-88120400	Weak transcription	Fetal Stomach	stomach
19	chr3:88110000-88120400	Weak transcription	Fetal Thymus	thymus
20	chr3:88110000-88121000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr3:88110200-88115600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:88110200-88117200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:88110200-88124200	Weak transcription	Fetal Kidney	kidney
24	chr3:88110400-88120200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:88110800-88113800	Enhancers	Primary T cells from cord blood	blood
26	chr3:88111200-88115400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:88111200-88117800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:88111400-88113400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:88111400-88113600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:88111400-88113600	Weak transcription	Brain Substantia Nigra	brain
31	chr3:88111400-88114000	Enhancers	Primary hematopoietic stem cells	blood
32	chr3:88111400-88115600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:88111400-88116400	Weak transcription	Right Ventricle	heart
34	chr3:88111400-88117200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:88111400-88121600	Weak transcription	Fetal Brain Male	brain
36	chr3:88111400-88124200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr3:88111400-88133600	Weak transcription	Brain Angular Gyrus	brain
38	chr3:88111400-88136200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:88111400-88136200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:88111600-88112800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:88111600-88112800	Weak transcription	Small Intestine	intestine
42	chr3:88111600-88112800	Weak transcription	K562	blood
43	chr3:88111600-88112800	Weak transcription	NHDF-Ad	bronchial
44	chr3:88111600-88113000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:88111600-88113000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:88111600-88113000	Weak transcription	Brain Hippocampus Middle	brain
47	chr3:88111600-88113400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr3:88111600-88113400	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:88111600-88113800	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr3:88111600-88113800	Enhancers	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links