Variant report

Variant	rs11808883
Chromosome Location	chr1:197166922-197166923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAL1	chr1:197166885-197167114	K562	blood:	n/a	n/a
2	MAZ	chr1:197166551-197167191	K562	blood:	n/a	n/a
3	MXI1	chr1:197166903-197167103	GM12878	blood:	n/a	n/a
4	BHLHE40	chr1:197166826-197167245	K562	blood:	n/a	n/a
5	RCOR1	chr1:197166620-197167229	K562	blood:	n/a	n/a
6	JUND	chr1:197166714-197167569	K562	blood:	n/a	chr1:197167398-197167410
7	STAT3	chr1:197166917-197167216	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:197152680..197155309-chr1:197165847..197169413,3	MCF-7	breast:
2	chr1:197114701..197116703-chr1:197164093..197167028,2	MCF-7	breast:
3	chr1:197161517..197163826-chr1:197164890..197167674,2	K562	blood:
4	chr1:197165634..197167836-chr1:197312237..197315122,2	K562	blood:
5	chr1:197159273..197161304-chr1:197164955..197167252,3	K562	blood:
6	chr1:197165132..197167397-chr1:197181290..197183417,2	K562	blood:
7	chr1:197110180..197113762-chr1:197163844..197167381,3	K562	blood:
8	chr1:197114016..197117152-chr1:197163839..197167436,4	K562	blood:

No data

Variant related genes	Relation type
CRB1	TF binding region
ENSG00000066279	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1034162	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10429911	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10494748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10494749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10494750	1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10494751	0.81[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10732295	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10732296	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10801594	1.00[CHB][hapmap]
rs11800461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11801772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11803081	1.00[AMR][1000 genomes]
rs11808524	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11809963	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11810041	0.85[AMR][1000 genomes]
rs11811295	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11811814	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1337165	1.00[AMR][1000 genomes]
rs1412631	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1415217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1556763	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1571964	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16841212	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841214	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841220	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841270	1.00[AMR][1000 genomes]
rs1759013	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1794003	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4915378	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs59820773	1.00[ASN][1000 genomes]
rs61170532	1.00[AMR][1000 genomes]
rs61172533	1.00[ASN][1000 genomes]
rs6677082	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6700604	1.00[ASN][1000 genomes]
rs6702338	1.00[ASN][1000 genomes]
rs6702739	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6703400	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7520503	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7534439	1.00[JPT][hapmap]
rs7535048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758990	chr1:196590837-197169772	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv427897	chr1:196590837-197169772	Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv2757767	chr1:196977799-197169772	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv873071	chr1:197079671-197187605	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv873072	chr1:197079671-197221248	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv548871	chr1:197106604-197168233	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv873073	chr1:197107074-197221248	Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197116600-197169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:197125400-197168400	Weak transcription	Psoas Muscle	Psoas
3	chr1:197125600-197169600	Weak transcription	Esophagus	oesophagus
4	chr1:197126400-197169600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:197152400-197168600	Weak transcription	Stomach Mucosa	stomach
6	chr1:197157400-197167000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:197157400-197168400	Weak transcription	Left Ventricle	heart
8	chr1:197157400-197169400	Weak transcription	Colonic Mucosa	Colon
9	chr1:197157400-197169600	Weak transcription	Pancreas	Pancrea
10	chr1:197157600-197167000	Weak transcription	HMEC	breast
11	chr1:197157600-197167000	Weak transcription	HUVEC	blood vessel
12	chr1:197157600-197167600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:197159400-197169600	Weak transcription	Gastric	stomach
14	chr1:197159400-197169800	Weak transcription	Lung	lung
15	chr1:197159600-197167000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:197159600-197167000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:197159600-197167800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:197159600-197168600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:197159600-197169200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:197159600-197169800	Weak transcription	Spleen	Spleen
21	chr1:197159800-197168600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:197159800-197169600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:197160600-197167000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:197160600-197167200	Weak transcription	Fetal Intestine Large	intestine
25	chr1:197160600-197169200	Weak transcription	Fetal Stomach	stomach
26	chr1:197161000-197167400	Weak transcription	Fetal Muscle Leg	muscle
27	chr1:197161000-197168200	Weak transcription	Fetal Thymus	thymus
28	chr1:197161000-197169200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:197161000-197169400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:197161000-197169400	Weak transcription	Placenta	Placenta
31	chr1:197161200-197168600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr1:197161600-197168800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:197162800-197167200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr1:197163400-197169400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:197163600-197168800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:197163800-197167000	Enhancers	NHDF-Ad	bronchial
37	chr1:197164000-197168600	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr1:197164000-197168800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr1:197164000-197169200	Active TSS	GM12878-XiMat	blood
40	chr1:197164200-197167000	Enhancers	Brain Angular Gyrus	brain
41	chr1:197164600-197168400	Enhancers	Hela-S3	cervix
42	chr1:197164800-197167200	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr1:197164800-197169400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr1:197165000-197169400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:197165600-197169200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:197165800-197167000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:197165800-197167000	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr1:197165800-197167000	Enhancers	Fetal Lung	lung
49	chr1:197165800-197167200	Enhancers	Small Intestine	intestine
50	chr1:197166200-197167400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links