Variant report

Variant	rs1727302
Chromosome Location	chr12:123632930-123632931
allele	C/T
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123625936..123634145-chr12:123634916..123640513,10	K562	blood:
2	chr12:123624513..123626615-chr12:123631268..123633682,3	K562	blood:
3	chr12:123527304..123529634-chr12:123630952..123633326,2	MCF-7	breast:
4	chr12:123616507..123619286-chr12:123631305..123632986,2	K562	blood:
5	chr12:123616297..123618408-chr12:123632574..123634282,2	MCF-7	breast:
6	chr12:123573881..123576493-chr12:123631498..123633206,2	K562	blood:
7	chr12:123603146..123605205-chr12:123632203..123634341,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 155 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs1047158	0.84[EUR][1000 genomes]
rs1051431	0.89[CEU][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs1051434	0.81[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1060105	0.82[TSI][hapmap]
rs10732573	0.90[CEU][hapmap]
rs10744147	0.81[EUR][1000 genomes]
rs10772993	0.83[EUR][1000 genomes]
rs10772998	0.89[CEU][hapmap]
rs10773002	0.85[CEU][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs10773003	0.84[JPT][hapmap]
rs10773005	0.84[JPT][hapmap]
rs10773921	0.83[CHB][hapmap];0.82[TSI][hapmap]
rs10846486	0.89[CEU][hapmap]
rs10848428	0.83[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs11057189	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11057192	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs11057207	0.80[EUR][1000 genomes]
rs11057251	0.84[JPT][hapmap]
rs11057276	0.84[JPT][hapmap]
rs1106240	0.89[CEU][hapmap];0.92[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs1106241	0.82[ASW][hapmap];0.89[CEU][hapmap];0.92[GIH][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap];0.84[EUR][1000 genomes]
rs11608305	0.84[JPT][hapmap]
rs11608811	0.83[CHB][hapmap];0.82[TSI][hapmap]
rs12298826	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs12316131	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs12317452	0.84[JPT][hapmap]
rs12322888	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs12366872	0.84[JPT][hapmap]
rs12425009	0.83[CHB][hapmap];0.82[TSI][hapmap]
rs1260294	0.84[CEU][hapmap]
rs12817892	0.84[CEU][hapmap]
rs1402274	0.89[CEU][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs1463877	0.84[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs1533703	0.82[CEU][hapmap]
rs1568427	0.81[CEU][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs1569068	0.89[ASW][hapmap];0.89[CEU][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs1609520	0.90[CEU][hapmap];0.89[TSI][hapmap]
rs1611973	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1615350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1616131	0.83[EUR][1000 genomes]
rs1616181	0.83[EUR][1000 genomes]
rs1617156	0.84[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs1617434	0.81[EUR][1000 genomes]
rs1621194	0.83[EUR][1000 genomes]
rs1627724	0.84[EUR][1000 genomes]
rs1716157	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs1716160	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs1716164	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs1716165	0.89[CEU][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs1716167	0.89[CEU][hapmap];0.92[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs1716168	0.89[CEU][hapmap];0.92[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs1716170	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs1716171	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs1716175	0.89[CEU][hapmap]
rs1716176	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1716177	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1716184	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1716185	0.82[EUR][1000 genomes]
rs1727293	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1727294	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1727295	0.90[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs1727296	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs1727301	0.84[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1727305	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1727306	0.89[CEU][hapmap]
rs1727307	0.83[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs1727309	0.89[CEU][hapmap]
rs1727312	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1727313	0.89[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs1727314	0.83[EUR][1000 genomes]
rs1727315	0.89[CEU][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs1727316	0.83[EUR][1000 genomes]
rs1727317	0.81[EUR][1000 genomes]
rs1727318	0.81[EUR][1000 genomes]
rs1727319	0.90[EUR][1000 genomes]
rs1727320	0.89[CEU][hapmap]
rs1727323	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs1727324	0.89[CEU][hapmap]
rs1727325	0.89[CEU][hapmap]
rs1727331	0.90[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs1727334	0.81[CEU][hapmap]
rs1790089	0.80[EUR][1000 genomes]
rs1790090	0.84[EUR][1000 genomes]
rs1790094	0.83[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs1790095	0.89[CEU][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs1790098	0.89[CEU][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs1790100	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs1790104	0.90[JPT][hapmap]
rs1790106	0.83[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs1790108	0.89[CEU][hapmap];0.92[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs1790109	0.84[EUR][1000 genomes]
rs1790116	0.84[CEU][hapmap];0.92[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs1790121	0.83[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs1790123	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs1790131	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs1879380	0.89[CEU][hapmap]
rs1969354	0.84[CEU][hapmap]
rs1980252	0.84[CEU][hapmap]
rs2049114	0.89[CEU][hapmap]
rs2102949	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2337934	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs2510885	0.81[EUR][1000 genomes]
rs2682427	0.84[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2682429	0.84[EUR][1000 genomes]
rs2682434	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs2695478	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs2695481	0.84[EUR][1000 genomes]
rs2695482	0.89[CEU][hapmap];0.90[YRI][hapmap];0.84[EUR][1000 genomes]
rs2851438	0.84[EUR][1000 genomes]
rs2851443	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2851447	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3018098	0.81[EUR][1000 genomes]
rs3088303	0.84[JPT][hapmap]
rs3759111	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs3759113	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs3759115	0.83[CHB][hapmap];0.82[TSI][hapmap]
rs3897102	0.83[CHB][hapmap]
rs4148863	0.83[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs4372492	0.89[CEU][hapmap]
rs4460848	1.00[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4759367	0.82[JPT][hapmap]
rs4759371	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs4759377	0.84[JPT][hapmap]
rs4759407	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs4759409	0.84[CEU][hapmap]
rs4759415	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs520088	0.84[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs58991895	0.89[ASN][1000 genomes]
rs61041384	0.87[ASN][1000 genomes]
rs61187102	0.86[ASN][1000 genomes]
rs641760	0.84[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs655293	0.84[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs7135296	0.83[CHB][hapmap];0.82[TSI][hapmap]
rs7296418	0.81[TSI][hapmap]
rs7304782	0.90[CEU][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs7305511	0.83[CHB][hapmap];0.82[TSI][hapmap]
rs7313483	0.89[CEU][hapmap]
rs7315453	0.84[JPT][hapmap]
rs7953929	0.89[CEU][hapmap]
rs7959415	0.84[JPT][hapmap]
rs7972811	0.84[JPT][hapmap]
rs883263	0.83[GIH][hapmap];0.81[TSI][hapmap]
rs884548	0.89[CEU][hapmap];0.90[YRI][hapmap];0.84[EUR][1000 genomes]
rs937564	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs941305	0.89[CEU][hapmap]
rs941306	0.89[CEU][hapmap]
rs949142	0.84[EUR][1000 genomes]
rs949143	0.83[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]

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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1727302	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs1727302	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs1727302	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs1727302	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs1727302	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs1727302	CCDC92	cis	cerebellum	SCAN
rs1727302	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs1727302	ABCB9	cis	Heart Left Ventricle	GTEx
rs1727302	PITPNM2	cis	cerebellum	SCAN
rs1727302	ABCB9	cis	Skin Sun Exposed Lower leg	GTEx
rs1727302	ANAPC5	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123594600-123634000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:123618000-123634200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:123625000-123633600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:123625400-123633800	Weak transcription	Fetal Brain Male	brain
5	chr12:123625400-123634600	Weak transcription	Aorta	Aorta
6	chr12:123627000-123633200	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:123627000-123634200	Weak transcription	NHEK	skin
8	chr12:123627000-123634800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:123627200-123634000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:123627200-123634000	Weak transcription	HMEC	breast
11	chr12:123627200-123634000	Weak transcription	HSMMtube	muscle
12	chr12:123627400-123633200	Weak transcription	Fetal Brain Female	brain
13	chr12:123627800-123633200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr12:123627800-123633600	Weak transcription	Stomach Mucosa	stomach
15	chr12:123627800-123633800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:123627800-123634000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr12:123627800-123634400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:123628000-123633200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:123628000-123633400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:123628000-123633600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:123628000-123633600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:123628000-123633600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr12:123628000-123634200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:123628200-123633000	Weak transcription	Fetal Heart	heart
25	chr12:123628200-123633400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:123628200-123633400	Weak transcription	Fetal Intestine Large	intestine
27	chr12:123628200-123633600	Weak transcription	Fetal Intestine Small	intestine
28	chr12:123628200-123633800	Weak transcription	Fetal Stomach	stomach
29	chr12:123628400-123633200	Weak transcription	Right Atrium	heart
30	chr12:123628400-123633400	Weak transcription	Placenta	Placenta
31	chr12:123628400-123633600	Weak transcription	Psoas Muscle	Psoas
32	chr12:123628400-123633800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:123628400-123634000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:123628600-123633200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr12:123628600-123633200	Weak transcription	Lung	lung
36	chr12:123628600-123633400	Weak transcription	Gastric	stomach
37	chr12:123628600-123633600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:123628600-123633600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr12:123628600-123633800	Weak transcription	Adipose Nuclei	Adipose
40	chr12:123628600-123634000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:123628800-123633000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr12:123628800-123633200	Weak transcription	Brain Angular Gyrus	brain
43	chr12:123628800-123633200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr12:123628800-123633200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr12:123628800-123633400	Weak transcription	Brain Substantia Nigra	brain
46	chr12:123628800-123633800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr12:123628800-123633800	Weak transcription	NHLF	lung
48	chr12:123628800-123634400	Weak transcription	Esophagus	oesophagus
49	chr12:123629000-123633000	Weak transcription	Right Ventricle	heart
50	chr12:123629000-123633200	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links