Variant report

Variant	rs884548
Chromosome Location	chr12:123634122-123634123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123634064..123637299-chr12:123639365..123644376,5	K562	blood:
2	chr12:123318440..123320805-chr12:123633475..123636263,2	MCF-7	breast:
3	chr12:123625936..123634145-chr12:123634916..123640513,10	K562	blood:
4	chr12:123632948..123634613-chr12:123717747..123719847,2	K562	blood:
5	chr12:123633130..123634910-chr12:123716201..123717715,2	K562	blood:
6	chr12:123634053..123636860-chr12:123645111..123649875,5	MCF-7	breast:
7	chr12:123633368..123635688-chr12:123701614..123704544,2	MCF-7	breast:
8	chr12:123616297..123618408-chr12:123632574..123634282,2	MCF-7	breast:
9	chr12:123463900..123466022-chr12:123633750..123636695,4	K562	blood:
10	chr12:123463900..123467066-chr12:123633750..123636695,4	K562	blood:
11	chr12:123603146..123605205-chr12:123632203..123634341,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130921	Chromatin interaction
ENSG00000182196	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000150967	Chromatin interaction

Extended variants
information (count: 161 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:154)

rs_ID	r²[population]
rs1047158	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060105	0.89[CEU][hapmap]
rs10732573	0.81[CEU][hapmap]
rs10744147	0.94[EUR][1000 genomes]
rs10772993	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772995	0.93[EUR][1000 genomes]
rs10772996	0.80[EUR][1000 genomes]
rs10772998	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs10846478	0.93[EUR][1000 genomes]
rs10846486	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10846487	0.81[EUR][1000 genomes]
rs11057189	0.80[EUR][1000 genomes]
rs11057192	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs11057204	0.83[EUR][1000 genomes]
rs11057206	0.84[EUR][1000 genomes]
rs11057210	0.83[EUR][1000 genomes]
rs1106240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11830103	0.85[CEU][hapmap]
rs12298826	0.94[CEU][hapmap]
rs12304248	0.89[CEU][hapmap]
rs12316131	0.94[CEU][hapmap]
rs12322888	0.94[CEU][hapmap]
rs1260294	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs12817892	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12818067	0.82[EUR][1000 genomes]
rs12829456	0.82[EUR][1000 genomes]
rs1402274	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1463877	0.94[CEU][hapmap]
rs1533703	0.94[CEU][hapmap]
rs1569068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1609520	0.80[CEU][hapmap]
rs1615350	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs1615694	0.92[EUR][1000 genomes]
rs1616131	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616181	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1617156	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs1617434	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1618679	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1621194	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626899	0.91[EUR][1000 genomes]
rs1627724	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630693	0.92[EUR][1000 genomes]
rs1630905	0.93[EUR][1000 genomes]
rs1716156	0.89[EUR][1000 genomes]
rs1716157	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1716158	0.86[EUR][1000 genomes]
rs1716159	0.93[EUR][1000 genomes]
rs1716160	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1716164	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1716165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716170	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1716171	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1716172	0.87[EUR][1000 genomes]
rs1716173	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1716175	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1716176	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1716177	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1716182	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1716183	0.93[ASN][1000 genomes]
rs1716185	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727290	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1727294	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1727296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1727300	0.91[EUR][1000 genomes]
rs1727302	0.89[CEU][hapmap];0.90[YRI][hapmap];0.84[EUR][1000 genomes]
rs1727306	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1727309	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1727310	0.91[EUR][1000 genomes]
rs1727313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727314	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727316	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727317	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1727318	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1727320	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1727322	0.87[EUR][1000 genomes]
rs1727323	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1727324	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1727325	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1727331	0.80[CEU][hapmap]
rs1727334	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs1790086	0.93[EUR][1000 genomes]
rs1790087	0.93[EUR][1000 genomes]
rs1790089	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1790090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790095	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1790098	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1790100	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1790101	0.92[EUR][1000 genomes]
rs1790102	0.92[EUR][1000 genomes]
rs1790108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790109	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790116	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790119	0.83[EUR][1000 genomes]
rs1790120	0.89[EUR][1000 genomes]
rs1790123	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1790124	0.90[EUR][1000 genomes]
rs1790125	0.85[EUR][1000 genomes]
rs1790130	0.91[EUR][1000 genomes]
rs1790131	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1879380	1.00[CEU][hapmap]
rs1969354	0.94[CEU][hapmap]
rs1980252	0.94[CEU][hapmap]
rs2049114	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2337934	0.94[CEU][hapmap]
rs2510885	0.96[EUR][1000 genomes]
rs2682425	0.85[EUR][1000 genomes]
rs2682429	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682430	0.91[EUR][1000 genomes]
rs2682431	0.93[EUR][1000 genomes]
rs2682433	0.91[EUR][1000 genomes]
rs2682434	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2695476	0.91[EUR][1000 genomes]
rs2695478	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2695479	0.91[EUR][1000 genomes]
rs2695480	0.90[EUR][1000 genomes]
rs2695481	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851435	0.89[EUR][1000 genomes]
rs2851436	0.91[EUR][1000 genomes]
rs2851438	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851441	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2851447	0.88[CEU][hapmap]
rs2851450	0.93[EUR][1000 genomes]
rs2851451	0.93[EUR][1000 genomes]
rs2947099	0.91[EUR][1000 genomes]
rs2950537	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3018098	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34341465	0.82[EUR][1000 genomes]
rs4372492	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4460848	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs4759371	0.94[CEU][hapmap]
rs4759409	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs4759415	0.94[CEU][hapmap]
rs520088	0.94[CEU][hapmap]
rs58809476	0.82[EUR][1000 genomes]
rs641760	0.94[CEU][hapmap]
rs655293	0.94[CEU][hapmap]
rs7132277	0.89[CEU][hapmap]
rs7299943	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7304782	0.80[CEU][hapmap]
rs7313483	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs7953929	1.00[CEU][hapmap]
rs7980687	0.89[CEU][hapmap]
rs883263	0.88[CEU][hapmap]
rs937564	0.94[CEU][hapmap]
rs941305	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs941306	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs949142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9795522	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv870326	chr12:123585990-123719323	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	esv2761773	chr12:123616003-123723460	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs884548	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs884548	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs884548	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs884548	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs884548	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs884548	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs884548	RP11-282O18.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123618000-123634200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr12:123625400-123634600	Weak transcription	Aorta	Aorta
3	chr12:123627000-123634200	Weak transcription	NHEK	skin
4	chr12:123627000-123634800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:123627800-123634400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:123628000-123634200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:123628800-123634400	Weak transcription	Esophagus	oesophagus
8	chr12:123629000-123634200	Weak transcription	Osteobl	bone
9	chr12:123631200-123634400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
10	chr12:123631200-123634800	Transcr. at gene 5' and 3'	Thymus	Thymus
11	chr12:123631600-123634200	Enhancers	Liver	Liver
12	chr12:123631600-123634400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:123631800-123634200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr12:123632000-123634600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:123632200-123634400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr12:123632400-123634400	Enhancers	Primary hematopoietic stem cells	blood
17	chr12:123632600-123634800	Enhancers	Spleen	Spleen
18	chr12:123632800-123634400	Enhancers	Primary T cells fromperipheralblood	blood
19	chr12:123632800-123634400	Enhancers	Left Ventricle	heart
20	chr12:123633200-123634200	Enhancers	Lung	lung
21	chr12:123633200-123634400	Enhancers	Pancreas	Pancrea
22	chr12:123633200-123634600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr12:123633200-123634600	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr12:123633200-123634600	Enhancers	Right Atrium	heart
25	chr12:123633400-123634400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:123633400-123634400	Enhancers	Brain Substantia Nigra	brain
27	chr12:123633400-123634400	Enhancers	Gastric	stomach
28	chr12:123633400-123634400	Flanking Active TSS	HepG2	liver
29	chr12:123633400-123634600	Enhancers	Fetal Intestine Large	intestine
30	chr12:123633400-123634600	Enhancers	Placenta	Placenta
31	chr12:123633600-123634600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:123633600-123634800	Enhancers	Placenta Amnion	Placenta Amnion
33	chr12:123633800-123634200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
34	chr12:123633800-123634200	Enhancers	Primary B cells from peripheral blood	blood
35	chr12:123633800-123634200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:123633800-123634200	Weak transcription	Psoas Muscle	Psoas
37	chr12:123633800-123634200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr12:123633800-123634200	Enhancers	Right Ventricle	heart
39	chr12:123633800-123634400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:123633800-123634400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:123633800-123634400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:123633800-123634400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:123633800-123634400	Enhancers	Fetal Kidney	kidney
44	chr12:123633800-123634400	Enhancers	HUVEC	blood vessel
45	chr12:123633800-123634400	Enhancers	NH-A	brain
46	chr12:123633800-123634600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:123633800-123634600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:123633800-123634600	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr12:123633800-123634600	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr12:123633800-123634600	Enhancers	Small Intestine	intestine

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