Variant report

Variant	rs12684823
Chromosome Location	chr9:97667934-97667935
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97665297..97668002-chr9:97676455..97679387,2	MCF-7	breast:
2	chr9:97664999..97668189-chr9:97674058..97675675,3	MCF-7	breast:
3	chr9:97666485..97669668-chr9:97669881..97673620,4	MCF-7	breast:
4	chr9:97577751..97580681-chr9:97667871..97670064,2	MCF-7	breast:
5	chr9:97667630..97670627-chr9:97680732..97685586,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs16911702	1.00[YRI][hapmap]
rs16911824	0.87[ASN][1000 genomes]
rs3802455	0.80[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs4744376	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs4744381	0.84[CHB][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12684823	SYK	cis	parietal	SCAN
rs12684823	ABCG2	trans	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97633400-97671800	Weak transcription	Esophagus	oesophagus
2	chr9:97655800-97668400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:97656400-97669000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:97658800-97668400	Weak transcription	Pancreas	Pancrea
5	chr9:97660800-97702400	Weak transcription	Primary B cells from cord blood	blood
6	chr9:97661600-97686200	Weak transcription	Primary T cells from cord blood	blood
7	chr9:97662400-97678600	Enhancers	Brain Substantia Nigra	brain
8	chr9:97662600-97669600	Weak transcription	Right Atrium	heart
9	chr9:97662600-97670000	Weak transcription	Fetal Intestine Small	intestine
10	chr9:97662600-97680400	Enhancers	Brain Hippocampus Middle	brain
11	chr9:97662800-97669200	Weak transcription	Lung	lung
12	chr9:97662800-97670000	Weak transcription	Fetal Intestine Large	intestine
13	chr9:97663400-97669000	Weak transcription	Fetal Muscle Leg	muscle
14	chr9:97663400-97669200	Weak transcription	Fetal Heart	heart
15	chr9:97663400-97671200	Enhancers	HepG2	liver
16	chr9:97663600-97668000	Enhancers	NHLF	lung
17	chr9:97663600-97669000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr9:97663600-97669600	Weak transcription	Fetal Stomach	stomach
19	chr9:97663800-97669600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr9:97664400-97669600	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:97664600-97668200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:97664600-97669000	Weak transcription	Stomach Mucosa	stomach
23	chr9:97664800-97668200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr9:97664800-97669000	Weak transcription	Fetal Kidney	kidney
25	chr9:97664800-97669200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr9:97664800-97669600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr9:97664800-97669600	Weak transcription	Psoas Muscle	Psoas
28	chr9:97664800-97670000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr9:97664800-97670000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr9:97664800-97671800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr9:97664800-97672000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:97664800-97672200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr9:97664800-97673400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr9:97664800-97673400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr9:97664800-97674200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr9:97665000-97669000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr9:97665000-97669000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr9:97665000-97669000	Weak transcription	Fetal Lung	lung
39	chr9:97665000-97669200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:97665200-97674200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:97665400-97674200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr9:97665800-97669200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr9:97666000-97672000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:97666000-97678600	Enhancers	Brain Cingulate Gyrus	brain
45	chr9:97666200-97668400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr9:97666200-97668400	Weak transcription	Ovary	ovary
47	chr9:97666400-97668000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:97666400-97668000	Flanking Active TSS	A549	lung
49	chr9:97666600-97668800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr9:97666600-97669000	Weak transcription	Placenta	Placenta

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