Variant report

Variant	rs12958417
Chromosome Location	chr18:9836752-9836753
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9835743..9838576-chr18:9911593..9914261,2	MCF-7	breast:
2	chr18:9835315..9836905-chr18:9908815..9911185,2	K562	blood:
3	chr18:9835909..9838532-chr18:9841261..9843750,2	MCF-7	breast:
4	chr18:9835907..9837430-chr18:9925064..9927802,2	K562	blood:
5	chr18:9836686..9839180-chr18:9928720..9931249,2	K562	blood:

Variant related genes	Relation type
ENSG00000272799	Chromatin interaction
ENSG00000101558	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10048278	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11872226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875078	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17508949	1.00[ASW][hapmap]
rs2215498	1.00[CHB][hapmap]
rs34797558	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35024660	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35732254	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62081240	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72959354	0.84[AMR][1000 genomes]
rs8082842	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469897	chr18:9674498-9870517	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv482461	chr18:9674498-9870517	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv833586	chr18:9783830-9971693	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv2761989	chr18:9834599-9837639	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12958417	KIAA0802	cis	parietal	SCAN
rs12958417	CIDEA	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9825400-9849800	Weak transcription	Gastric	stomach
2	chr18:9827800-9837800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr18:9828400-9838400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr18:9828400-9846000	Weak transcription	Pancreas	Pancrea
5	chr18:9828600-9838000	Weak transcription	HSMMtube	muscle
6	chr18:9829000-9838000	Weak transcription	HSMM	muscle
7	chr18:9829000-9841600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr18:9829000-9845200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr18:9829000-9848200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr18:9829400-9838000	Weak transcription	NH-A	brain
11	chr18:9829600-9838800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr18:9829600-9846600	Weak transcription	NHDF-Ad	bronchial
13	chr18:9830400-9839400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr18:9831200-9847200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr18:9831600-9852400	Weak transcription	A549	lung
16	chr18:9831800-9845200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr18:9832000-9838000	Weak transcription	Aorta	Aorta
18	chr18:9832400-9846600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr18:9832800-9837800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr18:9832800-9845000	Weak transcription	Osteobl	bone
21	chr18:9832800-9865000	Weak transcription	Spleen	Spleen
22	chr18:9833000-9846400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr18:9833200-9838200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr18:9833200-9842200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr18:9833400-9838000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr18:9833400-9838200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr18:9833400-9839400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr18:9833600-9838200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr18:9834000-9836800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr18:9834200-9837400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr18:9834600-9847400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr18:9834800-9837000	Enhancers	Esophagus	oesophagus
33	chr18:9834800-9837200	Enhancers	Stomach Smooth Muscle	stomach
34	chr18:9834800-9838200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr18:9834800-9838800	Enhancers	Fetal Muscle Leg	muscle
36	chr18:9835000-9836800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr18:9835000-9836800	Enhancers	Fetal Intestine Small	intestine
38	chr18:9835000-9837000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr18:9835000-9837000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr18:9835000-9837000	Enhancers	Brain Cingulate Gyrus	brain
41	chr18:9835000-9837000	Enhancers	Fetal Kidney	kidney
42	chr18:9835000-9837000	Enhancers	Ovary	ovary
43	chr18:9835000-9837000	Flanking Active TSS	NHEK	skin
44	chr18:9835000-9839600	Enhancers	Rectal Smooth Muscle	rectum
45	chr18:9835000-9840200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr18:9835200-9836800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr18:9835200-9837000	Enhancers	Fetal Brain Male	brain
48	chr18:9835200-9837000	Enhancers	Placenta Amnion	Placenta Amnion
49	chr18:9835400-9836800	Enhancers	Brain Hippocampus Middle	brain
50	chr18:9835400-9836800	Enhancers	Colon Smooth Muscle	Colon

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