Variant report

Variant	rs2272777
Chromosome Location	chr4:87967235-87967236
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:87967171-87970425	K562	blood:	n/a	n/a
2	POLR2A	chr4:87966958-87967673	HUVEC	blood vessel:	n/a	n/a
3	GATA2	chr4:87966675-87967329	SH-SY5Y	brain:	n/a	n/a
4	RCOR1	chr4:87967126-87967296	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:87965831..87967908-chr4:87968487..87970739,2	MCF-7	breast:
2	chr4:87965986..87967736-chr4:87989394..87991945,2	K562	blood:
3	chr4:87960365..87962821-chr4:87965345..87969600,5	K562	blood:
4	chr4:87964446..87966356-chr4:87966393..87968677,2	MCF-7	breast:
5	chr4:87963284..87965045-chr4:87965190..87967797,2	K562	blood:
6	chr4:87966822..87969393-chr4:87974722..87976813,3	K562	blood:
7	chr4:87963142..87968842-chr4:87969641..87976222,9	K562	blood:
8	chr4:87965646..87968151-chr4:87970035..87972421,2	K562	blood:

No data

Variant related genes	Relation type
AFF1	TF binding region
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10003332	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10008600	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10022960	0.89[ASN][1000 genomes]
rs1374936	0.80[ASN][1000 genomes]
rs1374937	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1584345	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs168161	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17012291	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972969	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2053774	0.88[ASN][1000 genomes]
rs2594276	0.83[CHB][hapmap]
rs2705617	0.80[ASN][1000 genomes]
rs340627	1.00[ASN][1000 genomes]
rs340628	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340629	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340632	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs340635	0.97[ASN][1000 genomes]
rs340640	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340644	0.91[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340645	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340646	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs340647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs340649	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340652	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4536897	0.82[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[ASN][1000 genomes]
rs4693155	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4693797	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs4693799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58317309	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6531943	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531944	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531945	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531947	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs6848056	0.90[ASN][1000 genomes]
rs6853011	0.89[ASN][1000 genomes]
rs72876089	0.89[EUR][1000 genomes]
rs73837575	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7685248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs895740	0.80[ASN][1000 genomes]
rs965824	0.91[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 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	chr4:87952600-87968000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:87953400-87967600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:87958800-87968000	Weak transcription	Esophagus	oesophagus
4	chr4:87960400-87968000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:87960400-87975400	Weak transcription	Brain Germinal Matrix	brain
6	chr4:87960800-87968000	Weak transcription	HSMM	muscle
7	chr4:87961000-87979200	Weak transcription	HSMMtube	muscle
8	chr4:87961200-87967800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr4:87962400-87967400	Enhancers	Right Ventricle	heart
10	chr4:87963200-87982200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:87963600-87967400	Enhancers	Pancreas	Pancrea
12	chr4:87963600-87967600	Enhancers	Fetal Heart	heart
13	chr4:87963800-87968000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:87964200-87968000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr4:87964600-87967400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:87964600-87967800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:87964600-87968000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr4:87964600-87968000	Weak transcription	Gastric	stomach
19	chr4:87964600-87995000	Weak transcription	Hela-S3	cervix
20	chr4:87964800-87979200	Weak transcription	A549	lung
21	chr4:87965200-87968000	Enhancers	Liver	Liver
22	chr4:87965400-87967400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:87965400-87967400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr4:87965400-87967400	Enhancers	Fetal Stomach	stomach
25	chr4:87965400-87967400	Genic enhancers	Fetal Thymus	thymus
26	chr4:87965600-87967400	Enhancers	Brain Anterior Caudate	brain
27	chr4:87965600-87967400	Enhancers	Fetal Intestine Large	intestine
28	chr4:87965600-87967400	Enhancers	Fetal Muscle Leg	muscle
29	chr4:87965600-87967600	Enhancers	Stomach Mucosa	stomach
30	chr4:87965800-87967400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:87965800-87967400	Flanking Active TSS	Colon Smooth Muscle	Colon
32	chr4:87965800-87967400	Enhancers	Fetal Intestine Small	intestine
33	chr4:87966000-87967600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr4:87966000-87967600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr4:87966000-87967800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:87966000-87967800	Weak transcription	HepG2	liver
37	chr4:87966000-87968000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:87966200-87967400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:87966200-87967400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr4:87966200-87968000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr4:87966200-87969800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr4:87966200-87979200	Weak transcription	NH-A	brain
43	chr4:87966400-87967400	Enhancers	Duodenum Mucosa	Duodenum
44	chr4:87966400-87967800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:87966400-87969800	Strong transcription	GM12878-XiMat	blood
46	chr4:87966600-87967400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:87966600-87967400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr4:87966600-87967600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr4:87966600-87967600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:87966600-87967800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links