Variant report

Variant	rs2274692
Chromosome Location	chr9:98224360-98224361
allele	C/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	POLR2A	chr9:98224260-98226090	GM12878	blood:	n/a	n/a
2	RELA	chr9:98224347-98225280	GM19099	blood:	n/a	n/a
3	JUN	chr9:98224318-98225728	K562	blood:	n/a	n/a
4	GATA1	chr9:98224155-98225483	K562	blood:	n/a	chr9:98225161-98225169 chr9:98225180-98225189 chr9:98225180-98225190 chr9:98225177-98225193 chr9:98225171-98225188 chr9:98225175-98225196
5	MTA3	chr9:98224242-98225790	GM12878	blood:	n/a	n/a
6	POLR2A	chr9:98224195-98225950	GM12878	blood:	n/a	n/a
7	GATA1	chr9:98224359-98225283	PBDE	blood:	n/a	chr9:98225161-98225169 chr9:98225180-98225189 chr9:98225180-98225190 chr9:98225177-98225193 chr9:98225171-98225188 chr9:98225175-98225196
8	RCOR1	chr9:98224262-98225400	K562	blood:	n/a	n/a
9	POLR2A	chr9:98224144-98226168	GM12878	blood:	n/a	n/a
10	POLR2A	chr9:98224335-98226055	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:98222888..98225027-chr9:98277335..98280257,3	K562	blood:
2	chr9:98223864..98226761-chr9:98228381..98231062,3	K562	blood:
3	chr9:98223555..98229775-chr9:98269693..98275962,10	K562	blood:
4	chr9:98222977..98229750-chr9:98267050..98274823,12	K562	blood:
5	chr12:53297243..53298949-chr9:98222802..98225552,2	MCF-7	breast:
6	chr9:98223412..98227347-chr9:98253313..98257210,3	K562	blood:
7	chr9:98223181..98225027-chr9:98277335..98280257,2	K562	blood:

Variant related genes	Relation type
PTCH1	TF binding region
ENSG00000271155	Chromatin interaction
ENSG00000185920	Chromatin interaction
ENSG00000170421	Chromatin interaction
ENSG00000271314	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2066829	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2236406	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236407	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2282042	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2297086	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2297088	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28495472	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28504650	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28557305	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28620532	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28701981	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv949520	chr9:98204199-98238358	Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1053762	chr9:98208542-98232120	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1047465	chr9:98217524-98228225	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98202000-98224600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:98204800-98224400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr9:98206000-98224400	Weak transcription	HUVEC	blood vessel
4	chr9:98206000-98237600	Weak transcription	Psoas Muscle	Psoas
5	chr9:98206600-98224600	Strong transcription	Aorta	Aorta
6	chr9:98206600-98225200	Strong transcription	Pancreas	Pancrea
7	chr9:98207200-98224400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr9:98207600-98224400	Strong transcription	Skeletal Muscle Male	skeletal muscle
9	chr9:98208000-98224400	Weak transcription	HSMM	muscle
10	chr9:98209600-98224400	Weak transcription	NHDF-Ad	bronchial
11	chr9:98211400-98224600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr9:98212000-98224600	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr9:98213200-98224600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr9:98213600-98224400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:98214200-98224400	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr9:98214200-98225400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:98215200-98224600	Weak transcription	Osteobl	bone
18	chr9:98218000-98224400	Strong transcription	HepG2	liver
19	chr9:98218800-98224400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr9:98218800-98227400	Genic enhancers	Fetal Stomach	stomach
21	chr9:98219000-98224400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:98219000-98224400	Weak transcription	NHEK	skin
23	chr9:98219400-98225400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr9:98219800-98224600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:98220000-98224600	Genic enhancers	Fetal Lung	lung
26	chr9:98220200-98225000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr9:98220600-98224400	Weak transcription	NH-A	brain
28	chr9:98220600-98224600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:98221200-98224600	Genic enhancers	Fetal Muscle Leg	muscle
30	chr9:98221400-98224400	Enhancers	NHLF	lung
31	chr9:98221400-98226400	Genic enhancers	Fetal Intestine Small	intestine
32	chr9:98221600-98224600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr9:98221800-98224400	Genic enhancers	Brain Cingulate Gyrus	brain
34	chr9:98221800-98224400	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr9:98221800-98224400	Bivalent Enhancer	Fetal Thymus	thymus
36	chr9:98221800-98224600	Weak transcription	Placenta	Placenta
37	chr9:98221800-98232400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr9:98222000-98224800	Enhancers	Fetal Brain Female	brain
39	chr9:98222200-98224400	Genic enhancers	Fetal Brain Male	brain
40	chr9:98222200-98224600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:98222200-98224600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:98222600-98224400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:98222800-98224600	Enhancers	Brain Germinal Matrix	brain
44	chr9:98223000-98224400	Genic enhancers	Primary T cells fromperipheralblood	blood
45	chr9:98223000-98224600	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr9:98223000-98224600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
47	chr9:98223200-98224400	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr9:98223200-98224600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:98223200-98224600	Genic enhancers	Rectal Mucosa Donor 29	rectum
50	chr9:98223200-98224600	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links