Variant report

Variant	rs28429424
Chromosome Location	chr3:98496095-98496096
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	HDAC2	chr3:98496037-98496615	HepG2	liver:	n/a	n/a
2	CEBPB	chr3:98496062-98496468	HepG2	liver:	n/a	n/a
3	FOXA1	chr3:98496060-98496561	HepG2	liver:	n/a	n/a
4	ZEB1	chr3:98495890-98497201	HepG2	liver:	n/a	chr3:98497020-98497032
5	FOXA1	chr3:98496073-98496661	HepG2	liver:	n/a	n/a
6	FOXA1	chr3:98496051-98496617	HepG2	liver:	n/a	n/a
7	ZEB1	chr3:98495953-98496661	HepG2	liver:	n/a	n/a
8	TEAD4	chr3:98495935-98496676	HepG2	liver:	n/a	n/a
9	EP300	chr3:98496078-98496465	HepG2	liver:	n/a	n/a
10	FOXA2	chr3:98496022-98496596	HepG2	liver:	n/a	n/a
11	EP300	chr3:98496023-98496640	HepG2	liver:	n/a	n/a
12	FOXA1	chr3:98496029-98496627	HepG2	liver:	n/a	n/a
13	SP1	chr3:98496044-98496597	HepG2	liver:	n/a	n/a
14	HNF4A	chr3:98496094-98496508	HepG2	liver:	n/a	n/a
15	FOXA2	chr3:98495728-98496808	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98494773..98497684-chr3:98500222..98503484,3	K562	blood:

Variant related genes	Relation type
PDLIM1P4	TF binding region
ENSG00000249274	Chromatin interaction
ENSG00000064225	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10084679	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13317610	0.82[ASN][1000 genomes]
rs13320266	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13320890	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13322253	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28417568	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28489284	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28821579	0.83[AMR][1000 genomes]
rs3796133	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56172805	0.82[ASN][1000 genomes]
rs59906228	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72932691	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72932700	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72934623	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72934641	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9810407	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9812438	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9818215	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9819309	0.83[AMR][1000 genomes]
rs9828045	0.83[AMR][1000 genomes]
rs9833945	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9836437	0.82[ASN][1000 genomes]
rs9836915	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9838166	0.82[ASN][1000 genomes]
rs9838238	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9838706	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9839559	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9848583	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9852537	0.83[AMR][1000 genomes]
rs9862660	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9870500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883751	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:98482600-98501800	Weak transcription	Fetal Stomach	stomach
3	chr3:98482800-98497400	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:98483000-98497400	Weak transcription	Spleen	Spleen
5	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
8	chr3:98483800-98496400	Weak transcription	Fetal Lung	lung
9	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:98484000-98498000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
14	chr3:98485000-98496200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:98488200-98496800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:98488600-98496200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:98488600-98497200	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:98488600-98497200	Weak transcription	Fetal Kidney	kidney
19	chr3:98489600-98497000	Weak transcription	Lung	lung
20	chr3:98489800-98496200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:98489800-98496400	Weak transcription	Placenta	Placenta
22	chr3:98489800-98496600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:98489800-98496600	Weak transcription	Adipose Nuclei	Adipose
24	chr3:98489800-98497000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:98489800-98497400	Weak transcription	Right Ventricle	heart
26	chr3:98489800-98497600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:98489800-98503000	Weak transcription	Psoas Muscle	Psoas
28	chr3:98490000-98496200	Weak transcription	Brain Substantia Nigra	brain
29	chr3:98490000-98496400	Weak transcription	Brain Anterior Caudate	brain
30	chr3:98490200-98496400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:98490400-98497400	Weak transcription	Fetal Brain Female	brain
33	chr3:98491600-98496600	Strong transcription	Primary hematopoietic stem cells	blood
34	chr3:98491600-98497400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:98493600-98496800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:98493800-98498400	Enhancers	HepG2	liver
38	chr3:98493800-98499600	Enhancers	Fetal Intestine Large	intestine
39	chr3:98494000-98497000	Strong transcription	Thymus	Thymus
40	chr3:98494400-98497200	Genic enhancers	Monocytes-CD14+_RO01746	blood
41	chr3:98494400-98498400	Enhancers	Fetal Intestine Small	intestine
42	chr3:98494600-98497600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:98494600-98499200	Genic enhancers	Primary monocytes fromperipheralblood	blood
44	chr3:98494600-98506000	Enhancers	Aorta	Aorta
45	chr3:98494800-98497000	Weak transcription	GM12878-XiMat	blood
46	chr3:98495200-98496800	Strong transcription	Fetal Thymus	thymus
47	chr3:98495200-98497600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:98495200-98498000	Enhancers	Pancreas	Pancrea
49	chr3:98495400-98497200	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr3:98495600-98496400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links