Variant report

Variant	rs5004460
Chromosome Location	chr2:191333533-191333534
allele	A/G
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	EP300	chr2:191333368-191335652	SK-N-SH	brain:	n/a	n/a
2	KAP1	chr2:191333489-191334329	HEK293	kidney:	n/a	n/a
3	TCF12	chr2:191333384-191334442	SK-N-SH	brain:	n/a	chr2:191334032-191334041 chr2:191333849-191333858
4	EP300	chr2:191333423-191334465	SK-N-SH	brain:	n/a	n/a
5	NFIC	chr2:191333380-191334410	ECC-1	luminal epithelium:	n/a	n/a
6	GATA3	chr2:191333433-191334958	SK-N-SH	brain:	n/a	n/a
7	NFIC	chr2:191333379-191335520	SK-N-SH	brain:	n/a	n/a
8	NFIC	chr2:191333395-191334437	ECC-1	luminal epithelium:	n/a	n/a
9	RCOR1	chr2:191333137-191334443	IMR90	lung:	n/a	n/a
10	TCF12	chr2:191333453-191334463	SK-N-SH	brain:	n/a	chr2:191334032-191334041 chr2:191333849-191333858
11	TCF12	chr2:191333517-191335063	A549	lung:	n/a	chr2:191334032-191334041 chr2:191333849-191333858

No.	Distal block	Cell Line	Cell type
1	chr2:191318515..191323057-chr2:191332501..191335066,4	MCF-7	breast:
2	chr2:191271631..191274450-chr2:191332507..191334267,2	MCF-7	breast:
3	chr2:191332610..191334392-chr2:191512174..191513999,2	K562	blood:

Variant related genes	Relation type
MFSD6	TF binding region
ENSG00000272979	Chromatin interaction
ENSG00000151690	Chromatin interaction
ENSG00000138386	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11683734	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11687958	1.00[ASN][1000 genomes]
rs11688236	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12105680	1.00[ASN][1000 genomes]
rs16832766	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17745140	1.00[ASN][1000 genomes]
rs2736620	1.00[ASN][1000 genomes]
rs4146925	0.89[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241290	0.89[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4303742	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4340551	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4434029	1.00[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4468843	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4513326	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4536676	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4585059	0.89[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4853511	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4853704	1.00[ASN][1000 genomes]
rs4853706	1.00[ASN][1000 genomes]
rs4853707	1.00[ASN][1000 genomes]
rs4853715	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs55942739	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56101840	1.00[ASN][1000 genomes]
rs56278738	1.00[ASN][1000 genomes]
rs6434392	0.88[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434393	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6434398	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707244	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728161	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736474	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744546	1.00[ASN][1000 genomes]
rs6751217	0.81[AFR][1000 genomes]
rs6755804	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570284	1.00[ASN][1000 genomes]
rs7586287	0.89[CEU][hapmap];1.00[ASN][1000 genomes]
rs7595579	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7600297	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7603228	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605008	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9967833	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33134	chr2:191318791-191365710	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191306600-191351000	Weak transcription	Pancreas	Pancrea
2	chr2:191313000-191333600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:191322000-191335800	Weak transcription	Esophagus	oesophagus
4	chr2:191322600-191335600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:191323000-191334600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:191323200-191335800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:191323400-191333600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr2:191325600-191335800	Weak transcription	Lung	lung
9	chr2:191325600-191346200	Weak transcription	Right Ventricle	heart
10	chr2:191327600-191353000	Weak transcription	Primary B cells from cord blood	blood
11	chr2:191328800-191334400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr2:191328800-191334600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr2:191329600-191334600	Weak transcription	Thymus	Thymus
14	chr2:191330000-191334800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr2:191330200-191334800	Enhancers	K562	blood
16	chr2:191330600-191335200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:191330800-191333800	Enhancers	Brain Hippocampus Middle	brain
18	chr2:191330800-191334800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:191330800-191335400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr2:191330800-191335400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr2:191331000-191333600	Enhancers	A549	lung
22	chr2:191331000-191334400	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr2:191331000-191334800	Enhancers	NHDF-Ad	bronchial
24	chr2:191331000-191335000	Enhancers	Brain Substantia Nigra	brain
25	chr2:191331000-191335200	Enhancers	Brain Cingulate Gyrus	brain
26	chr2:191331000-191335400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:191331000-191335400	Enhancers	Hela-S3	cervix
28	chr2:191331000-191335400	Enhancers	Osteobl	bone
29	chr2:191331200-191335400	Enhancers	NHLF	lung
30	chr2:191331200-191335600	Enhancers	Fetal Lung	lung
31	chr2:191331400-191333800	Enhancers	Right Atrium	heart
32	chr2:191331400-191333800	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr2:191331400-191334200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr2:191331400-191334400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr2:191331400-191334400	Enhancers	Fetal Brain Male	brain
36	chr2:191331400-191334800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr2:191331400-191334800	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr2:191331400-191335000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr2:191331400-191335000	Enhancers	Rectal Smooth Muscle	rectum
40	chr2:191331400-191335200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:191331400-191335200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:191331400-191335400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:191331400-191335400	Enhancers	Brain Angular Gyrus	brain
44	chr2:191331400-191335400	Enhancers	Fetal Heart	heart
45	chr2:191331400-191335400	Enhancers	Fetal Muscle Leg	muscle
46	chr2:191331400-191335400	Enhancers	Fetal Stomach	stomach
47	chr2:191331400-191335600	Enhancers	Colon Smooth Muscle	Colon
48	chr2:191331600-191333600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:191331600-191333800	Enhancers	Left Ventricle	heart
50	chr2:191331600-191334200	Enhancers	Fetal Brain Female	brain

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