Variant report

Variant	rs28441412
Chromosome Location	chr9:98223856-98223857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr9:98223840-98223980	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

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

No data

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

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs16909898	0.88[LWK][hapmap];0.87[MKK][hapmap]
rs16909938	1.00[CEU][hapmap]
rs2275104	1.00[CEU][hapmap]
rs2282040	0.88[LWK][hapmap]
rs28390100	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28429270	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28583690	0.91[AFR][1000 genomes]
rs28601668	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];0.80[MKK][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28676757	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28698995	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647396	1.00[CEU][hapmap]
rs4647399	1.00[CEU][hapmap]

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:118 , 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	chr9:98206600-98224000	Strong transcription	Adipose Nuclei	Adipose
6	chr9:98206600-98224600	Strong transcription	Aorta	Aorta
7	chr9:98206600-98225200	Strong transcription	Pancreas	Pancrea
8	chr9:98207200-98224400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr9:98207400-98224200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr9:98207600-98224400	Strong transcription	Skeletal Muscle Male	skeletal muscle
11	chr9:98208000-98224400	Weak transcription	HSMM	muscle
12	chr9:98208600-98224000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr9:98209600-98224000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr9:98209600-98224400	Weak transcription	NHDF-Ad	bronchial
15	chr9:98211200-98224200	Strong transcription	Left Ventricle	heart
16	chr9:98211400-98224600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr9:98212000-98224600	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr9:98213200-98224600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr9:98213600-98224000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:98213600-98224400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:98214200-98224200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr9:98214200-98224400	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr9:98214200-98225400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:98214400-98224200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:98214400-98224200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr9:98214800-98224000	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr9:98215200-98224600	Weak transcription	Osteobl	bone
28	chr9:98215400-98224200	Strong transcription	Right Ventricle	heart
29	chr9:98215600-98224200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr9:98216800-98224000	Weak transcription	Stomach Mucosa	stomach
31	chr9:98217600-98224200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr9:98218000-98224000	Strong transcription	Liver	Liver
33	chr9:98218000-98224400	Strong transcription	HepG2	liver
34	chr9:98218800-98224400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr9:98218800-98227400	Genic enhancers	Fetal Stomach	stomach
36	chr9:98219000-98224400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:98219000-98224400	Weak transcription	NHEK	skin
38	chr9:98219400-98224200	Weak transcription	Small Intestine	intestine
39	chr9:98219400-98225400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr9:98219800-98224600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr9:98220000-98224200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:98220000-98224600	Genic enhancers	Fetal Lung	lung
43	chr9:98220200-98224200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr9:98220200-98225000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:98220400-98224200	Weak transcription	HSMMtube	muscle
46	chr9:98220600-98224400	Weak transcription	NH-A	brain
47	chr9:98220600-98224600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:98221200-98224600	Genic enhancers	Fetal Muscle Leg	muscle
49	chr9:98221400-98224400	Enhancers	NHLF	lung
50	chr9:98221400-98226400	Genic enhancers	Fetal Intestine Small	intestine

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