Variant report

Variant	rs16911679
Chromosome Location	chr9:97522600-97522601
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	REST	chr9:97522000-97522920	H1-neurons	neurons:	n/a	n/a
2	RCOR1	chr9:97522303-97522822	K562	blood:	n/a	n/a

Variant related genes	Relation type
C9orf3	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12685623	1.00[AMR][1000 genomes]
rs16911665	1.00[AMR][1000 genomes]
rs16911678	1.00[ASW][hapmap];0.81[LWK][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28369711	1.00[AMR][1000 genomes]
rs28369787	1.00[AMR][1000 genomes]
rs28402403	1.00[AMR][1000 genomes]
rs3886567	0.82[ASW][hapmap]
rs3935327	1.00[AMR][1000 genomes]
rs56836699	1.00[AMR][1000 genomes]
rs56947670	1.00[AMR][1000 genomes]
rs58589586	1.00[AMR][1000 genomes]
rs59169111	1.00[AMR][1000 genomes]
rs60239830	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60774169	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7027571	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7044110	0.86[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72748515	1.00[AMR][1000 genomes]
rs73653486	1.00[AMR][1000 genomes]
rs73653488	1.00[AMR][1000 genomes]
rs7848054	1.00[AMR][1000 genomes]
rs7849970	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1041922	chr9:97444976-97536753	Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:128 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97489600-97524800	Weak transcription	Esophagus	oesophagus
2	chr9:97504400-97522600	Weak transcription	Ovary	ovary
3	chr9:97506200-97533400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:97506400-97526000	Weak transcription	Small Intestine	intestine
5	chr9:97509000-97522600	Weak transcription	Gastric	stomach
6	chr9:97509200-97536000	Weak transcription	Pancreas	Pancrea
7	chr9:97512600-97522600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:97512600-97522600	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:97512600-97522600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:97512600-97522800	Weak transcription	Fetal Kidney	kidney
11	chr9:97512600-97523200	Weak transcription	Fetal Brain Female	brain
12	chr9:97512600-97530400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr9:97512600-97540800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr9:97512600-97544600	Weak transcription	Psoas Muscle	Psoas
15	chr9:97518800-97522600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr9:97519000-97522800	Enhancers	Brain Hippocampus Middle	brain
17	chr9:97519000-97523000	Enhancers	Brain Angular Gyrus	brain
18	chr9:97519000-97523000	Enhancers	Brain Substantia Nigra	brain
19	chr9:97519200-97522600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:97519800-97531200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:97519800-97544600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:97520400-97525800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr9:97520400-97531800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:97520600-97522600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:97520600-97522600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:97520600-97529600	Weak transcription	NH-A	brain
27	chr9:97520600-97530600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr9:97520800-97522600	Weak transcription	Spleen	Spleen
29	chr9:97520800-97523000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:97520800-97531200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr9:97521200-97522600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:97521200-97523800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr9:97521200-97525000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr9:97521400-97522800	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr9:97521400-97527400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr9:97521600-97522600	Strong transcription	Adipose Nuclei	Adipose
37	chr9:97521600-97522600	Enhancers	Brain Cingulate Gyrus	brain
38	chr9:97521600-97523200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:97521600-97523400	Strong transcription	Rectal Smooth Muscle	rectum
40	chr9:97521600-97523600	Strong transcription	Fetal Stomach	stomach
41	chr9:97521600-97524000	Strong transcription	Fetal Thymus	thymus
42	chr9:97521600-97524200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr9:97521800-97523400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr9:97521800-97523400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:97521800-97523400	Strong transcription	Osteobl	bone
46	chr9:97521800-97523600	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr9:97521800-97524000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:97521800-97524200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr9:97521800-97541200	Weak transcription	Right Ventricle	heart
50	chr9:97522000-97522600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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