Variant report

Variant	rs2398780
Chromosome Location	chr9:95572381-95572382
allele	C/T
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	chr9:95572318-95572477	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr9:95572295-95572624	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr9:95572227-95572571	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr9:95571320-95572648	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95431331..95434473-chr9:95569877..95572688,3	MCF-7	breast:

Variant related genes	Relation type
ANKRD19P	TF binding region
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10821001	0.86[EUR][1000 genomes]
rs10821003	0.86[EUR][1000 genomes]
rs10821004	0.88[EUR][1000 genomes]
rs10821005	0.88[EUR][1000 genomes]
rs10821011	0.87[EUR][1000 genomes]
rs10821014	0.88[EUR][1000 genomes]
rs10992396	0.85[EUR][1000 genomes]
rs10992407	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs10992408	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs10992409	0.85[EUR][1000 genomes]
rs10992412	0.85[EUR][1000 genomes]
rs10992414	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs10992416	0.85[EUR][1000 genomes]
rs10992417	0.85[EUR][1000 genomes]
rs10992420	0.86[EUR][1000 genomes]
rs10992422	0.88[EUR][1000 genomes]
rs10992423	0.86[EUR][1000 genomes]
rs10992437	0.86[EUR][1000 genomes]
rs10992447	0.82[CEU][hapmap]
rs10992448	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs10992453	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs10992460	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs10992461	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs10992474	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10992475	0.95[ASN][1000 genomes]
rs10992476	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11533010	0.88[EUR][1000 genomes]
rs12057034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12236754	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs12238691	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs12684076	0.84[EUR][1000 genomes]
rs12684587	0.86[EUR][1000 genomes]
rs12685358	0.88[EUR][1000 genomes]
rs12686771	0.82[CEU][hapmap]
rs16908555	0.91[CEU][hapmap];0.84[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16908560	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1853427	0.98[ASN][1000 genomes]
rs1853428	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs1853429	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1974004	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs2181584	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs3739605	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs4141966	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56311406	0.89[EUR][1000 genomes]
rs57737182	0.89[EUR][1000 genomes]
rs58952648	0.88[EUR][1000 genomes]
rs60498616	0.88[EUR][1000 genomes]
rs7031163	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs72618187	0.96[ASN][1000 genomes]
rs753804	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs754600	0.81[EUR][1000 genomes]
rs7850075	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7855203	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7859967	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7860628	0.89[EUR][1000 genomes]
rs7863741	0.90[EUR][1000 genomes]
rs7869603	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831654	chr9:95542920-95720961	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv972420	chr9:95566045-95588965	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3373736	chr9:95569656-95572504	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95569400-95572400	Bivalent Enhancer	Fetal Brain Male	brain
2	chr9:95569400-95572400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr9:95569400-95572400	Bivalent Enhancer	Fetal Thymus	thymus
4	chr9:95569600-95572400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr9:95569600-95572400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
6	chr9:95569600-95572400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr9:95569600-95572400	Flanking Active TSS	Right Ventricle	heart
8	chr9:95569600-95572600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr9:95569800-95572400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:95569800-95572400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
11	chr9:95570000-95572400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr9:95570000-95572400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
13	chr9:95570000-95572400	Bivalent Enhancer	Liver	Liver
14	chr9:95570000-95572600	Bivalent Enhancer	Stomach Mucosa	stomach
15	chr9:95570200-95572400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
16	chr9:95570200-95572400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
17	chr9:95570400-95572400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr9:95570400-95572400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:95570400-95572400	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
20	chr9:95570600-95572400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
21	chr9:95570600-95572600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
22	chr9:95570600-95572600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:95571000-95572400	Bivalent/Poised TSS	Fetal Brain Female	brain
24	chr9:95571000-95572400	Bivalent Enhancer	Fetal Intestine Small	intestine
25	chr9:95571200-95572400	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:95571200-95572400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
27	chr9:95571200-95572400	Bivalent Enhancer	Fetal Heart	heart
28	chr9:95571400-95572400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr9:95571400-95572400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
30	chr9:95571400-95572600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
31	chr9:95571400-95572600	Bivalent Enhancer	Fetal Intestine Large	intestine
32	chr9:95571600-95572400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr9:95571600-95572400	Bivalent Enhancer	Small Intestine	intestine
34	chr9:95571800-95572400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
35	chr9:95571800-95572400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
36	chr9:95571800-95572400	Bivalent Enhancer	Adipose Nuclei	Adipose
37	chr9:95571800-95572400	Active TSS	Brain Angular Gyrus	brain
38	chr9:95571800-95572400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:95571800-95572400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
40	chr9:95571800-95572400	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr9:95571800-95572400	Bivalent Enhancer	Placenta	Placenta
42	chr9:95571800-95572400	Bivalent Enhancer	Left Ventricle	heart
43	chr9:95571800-95572400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
44	chr9:95571800-95572400	Bivalent Enhancer	Spleen	Spleen
45	chr9:95571800-95572400	Bivalent Enhancer	GM12878-XiMat	blood
46	chr9:95571800-95572600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
47	chr9:95571800-95572600	Bivalent Enhancer	Colon Smooth Muscle	Colon
48	chr9:95572000-95572400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:95572000-95572400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
50	chr9:95572000-95572400	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood

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