Variant report

Variant	rs10977154
Chromosome Location	chr9:8483347-8483348
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10115201	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs10115554	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs10117452	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs10117929	0.87[AFR][1000 genomes]
rs10117964	0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs10119472	0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs10124277	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs10977132	0.87[CEU][hapmap]
rs10977143	0.85[YRI][hapmap]
rs10977144	0.95[GIH][hapmap]
rs10977145	0.85[YRI][hapmap]
rs10977155	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12340876	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs1323578	0.85[CHD][hapmap]
rs1323592	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13283150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs13286274	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs13286656	0.87[CEU][hapmap]
rs13286908	0.87[CEU][hapmap];0.91[GIH][hapmap]
rs13290896	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs13291309	1.00[CEU][hapmap]
rs13292224	0.87[CEU][hapmap]
rs13294270	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13301764	0.87[CEU][hapmap]
rs13301979	0.95[GIH][hapmap]
rs16927991	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs16928002	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16928058	0.85[GIH][hapmap]
rs17650289	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2296102	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28588467	0.85[AFR][1000 genomes]
rs34190427	0.81[ASN][1000 genomes]
rs34599557	0.82[ASN][1000 genomes]
rs35777094	0.83[ASN][1000 genomes]
rs35929428	0.89[ASN][1000 genomes]
rs4338166	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56807533	0.85[AFR][1000 genomes]
rs58706764	0.83[AFR][1000 genomes]
rs62534023	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62534025	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62534026	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62534027	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62534040	0.80[ASN][1000 genomes]
rs62534042	0.80[ASN][1000 genomes]
rs745974	0.85[YRI][hapmap]
rs7863060	0.87[CEU][hapmap];0.90[GIH][hapmap]
rs7872008	0.85[CEU][hapmap]
rs9657635	0.90[YRI][hapmap]

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	nsv8414	chr9:7827373-8511613	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv892226	chr9:8435525-8522326	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv892228	chr9:8482778-8703733	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8419200-8491000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr9:8420600-8557600	Weak transcription	Aorta	Aorta
3	chr9:8424200-8485000	Weak transcription	Fetal Kidney	kidney
4	chr9:8434200-8485200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:8442200-8522200	Weak transcription	Liver	Liver
6	chr9:8448000-8494800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:8451400-8492000	Weak transcription	Psoas Muscle	Psoas
8	chr9:8464600-8494200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:8465800-8484000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:8468600-8484000	Weak transcription	Ovary	ovary
11	chr9:8473200-8483400	Weak transcription	Fetal Stomach	stomach
12	chr9:8473600-8491600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:8474000-8484000	Weak transcription	Brain Angular Gyrus	brain
14	chr9:8474400-8484800	Weak transcription	Fetal Heart	heart
15	chr9:8474400-8485200	Weak transcription	Brain Hippocampus Middle	brain
16	chr9:8475400-8483400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:8475600-8483400	Weak transcription	Brain Substantia Nigra	brain
18	chr9:8476400-8483400	Weak transcription	Fetal Muscle Leg	muscle
19	chr9:8476400-8483600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:8476800-8491400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:8477000-8491600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:8477600-8485000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:8478000-8484000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr9:8478000-8487000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:8478200-8504000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:8478400-8488800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr9:8478800-8483800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr9:8478800-8485000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr9:8478800-8485800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:8479000-8491800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr9:8479200-8483800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr9:8479200-8504000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr9:8479400-8485200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:8480400-8483800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr9:8480400-8484000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:8480600-8483800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr9:8480600-8484000	Weak transcription	Brain Anterior Caudate	brain
38	chr9:8481200-8500800	Weak transcription	Fetal Intestine Small	intestine
39	chr9:8481600-8488200	Strong transcription	Fetal Lung	lung
40	chr9:8482200-8486400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr9:8482200-8487000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr9:8482400-8491800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr9:8482600-8483400	Weak transcription	Fetal Brain Male	brain
44	chr9:8482600-8486000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:8482600-8486200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr9:8482800-8485000	Weak transcription	Fetal Brain Female	brain
47	chr9:8482800-8486200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr9:8483000-8483800	Weak transcription	Dnd41	blood
49	chr9:8483000-8484800	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links