Variant report

Variant	rs888198
Chromosome Location	chr12:12549503-12549504
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12549500..12552302-chr12:12715831..12718057,2	MCF-7	breast:
2	chr12:12546053..12553032-chr12:12712110..12718542,11	MCF-7	breast:
3	chr12:12548191..12550928-chr12:12559817..12561583,2	MCF-7	breast:
4	chr12:12547827..12551024-chr12:12713596..12715530,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111266	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11830917	1.00[CHD][hapmap]
rs11831188	1.00[ASN][1000 genomes]
rs11831555	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908006	0.91[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908019	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908222	1.00[CHD][hapmap]
rs17312912	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1861674	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2193269	0.83[AFR][1000 genomes]
rs2193270	0.80[YRI][hapmap]
rs3741797	1.00[CHD][hapmap]
rs4763288	1.00[JPT][hapmap]
rs4763289	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4763824	1.00[ASN][1000 genomes]
rs4763827	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4763828	1.00[ASN][1000 genomes]
rs4763831	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4763837	1.00[CHD][hapmap]
rs56089442	0.83[AFR][1000 genomes]
rs56261569	0.81[ASN][1000 genomes]
rs56796062	0.80[AFR][1000 genomes]
rs58218344	1.00[ASN][1000 genomes]
rs58529509	1.00[ASN][1000 genomes]
rs60022096	1.00[ASN][1000 genomes]
rs60363317	1.00[ASN][1000 genomes]
rs60971404	1.00[ASN][1000 genomes]
rs6488521	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488523	1.00[ASN][1000 genomes]
rs6488524	1.00[ASN][1000 genomes]
rs6488527	0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs7133988	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7134787	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7135655	0.93[YRI][hapmap]
rs714480	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300150	0.80[AFR][1000 genomes]
rs7306292	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309982	0.88[ASW][hapmap]
rs73287587	1.00[ASN][1000 genomes]
rs7957014	1.00[ASN][1000 genomes]
rs7973069	1.00[ASN][1000 genomes]
rs7975061	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7978842	1.00[ASN][1000 genomes]
rs7980390	1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898808	chr12:12463407-12549503	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS 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	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs888198	EPS8	cis	cerebellum	SCAN
rs888198	GUCY2C	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12511600-12550600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:12519200-12549800	Weak transcription	Aorta	Aorta
3	chr12:12521800-12556200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:12525400-12550200	Weak transcription	Fetal Stomach	stomach
5	chr12:12526400-12558800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:12532800-12556400	Weak transcription	Spleen	Spleen
7	chr12:12533400-12555800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr12:12533600-12555400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr12:12535400-12561400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr12:12537200-12576000	Weak transcription	Primary B cells from cord blood	blood
11	chr12:12538200-12551000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:12538400-12550200	Weak transcription	Primary T cells from cord blood	blood
13	chr12:12538400-12551600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:12538400-12552800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:12538400-12555400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:12538400-12556200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:12538600-12561800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:12538800-12551400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:12540200-12560600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:12540600-12556200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr12:12540800-12550800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:12540800-12551000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:12540800-12553800	Weak transcription	GM12878-XiMat	blood
24	chr12:12540800-12555400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr12:12541000-12550000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:12541000-12550200	Weak transcription	Hela-S3	cervix
27	chr12:12541000-12550600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:12541000-12551000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:12541000-12551000	Weak transcription	Small Intestine	intestine
30	chr12:12541400-12550000	Weak transcription	NHDF-Ad	bronchial
31	chr12:12541400-12550800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:12541400-12552600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr12:12541400-12562800	Weak transcription	Psoas Muscle	Psoas
34	chr12:12541800-12549800	Weak transcription	HSMMtube	muscle
35	chr12:12541800-12557200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr12:12542800-12551600	Weak transcription	Lung	lung
37	chr12:12543000-12558800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:12545600-12549800	Weak transcription	Fetal Kidney	kidney
39	chr12:12545600-12550200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:12545800-12555200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:12545800-12555200	Weak transcription	Fetal Intestine Small	intestine
42	chr12:12546000-12551400	Weak transcription	Fetal Intestine Large	intestine
43	chr12:12546000-12553200	Weak transcription	Right Atrium	heart
44	chr12:12546000-12556400	Weak transcription	K562	blood
45	chr12:12546200-12551400	Weak transcription	Left Ventricle	heart
46	chr12:12546200-12551400	Weak transcription	Pancreas	Pancrea
47	chr12:12547200-12556000	Weak transcription	Fetal Thymus	thymus
48	chr12:12547600-12551000	Weak transcription	Stomach Mucosa	stomach
49	chr12:12547600-12553400	Enhancers	Brain Substantia Nigra	brain
50	chr12:12547600-12555400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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