Variant report

Variant	rs2250026
Chromosome Location	chr12:124198405-124198406
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:124118119..124120182-chr12:124196891..124198426,2	K562	blood:
2	chr12:124180128..124181646-chr12:124198369..124200192,2	MCF-7	breast:
3	chr12:124116424..124121252-chr12:124194298..124198817,7	K562	blood:
4	chr12:124197317..124199862-chr12:124200055..124203034,3	K562	blood:
5	chr12:124157620..124159905-chr12:124196914..124199226,2	K562	blood:
6	chr12:124191295..124193347-chr12:124194777..124198625,4	MCF-7	breast:
7	chr12:124134030..124137334-chr12:124197093..124199913,4	MCF-7	breast:
8	chr12:124195456..124198460-chr12:124455550..124458339,3	MCF-7	breast:
9	chr12:124115420..124119615-chr12:124195159..124199573,8	MCF-7	breast:
10	chr12:124197009..124198582-chr12:124204764..124206340,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000111361	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000179195	Chromatin interaction
ENSG00000178882	Chromatin interaction
ENSG00000255839	Chromatin interaction
ENSG00000270095	Chromatin interaction
ENSG00000119242	Chromatin interaction
ENSG00000239215	Chromatin interaction

Extended variants
information (count: 150 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs1040156	0.84[CEU][hapmap]
rs1051793	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs1060637	0.89[CEU][hapmap]
rs10732574	0.81[CEU][hapmap]
rs10734905	0.80[CEU][hapmap]
rs10734906	0.81[CEU][hapmap]
rs10744160	0.81[CEU][hapmap]
rs10744162	0.81[CEU][hapmap]
rs10846535	0.96[CEU][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10846537	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs10846540	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10846541	0.91[ASN][1000 genomes]
rs10846546	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11057320	0.88[EUR][1000 genomes]
rs1139320	0.82[EUR][1000 genomes]
rs11572920	0.89[CEU][hapmap]
rs11572952	0.93[CEU][hapmap]
rs11609591	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs11611354	0.89[CEU][hapmap]
rs11612030	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs11612479	0.92[CEU][hapmap]
rs11612927	0.92[CEU][hapmap]
rs11613632	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs11614659	0.86[EUR][1000 genomes]
rs11829958	0.87[EUR][1000 genomes]
rs11833604	0.81[EUR][1000 genomes]
rs11834141	0.80[EUR][1000 genomes]
rs11834808	0.82[EUR][1000 genomes]
rs11837144	0.81[CEU][hapmap]
rs12580486	0.81[CEU][hapmap]
rs12811354	0.81[EUR][1000 genomes]
rs12813346	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12817757	0.89[CEU][hapmap]
rs12819746	0.88[EUR][1000 genomes]
rs12820195	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs12821219	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12821242	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs12822546	0.81[EUR][1000 genomes]
rs12823866	0.80[EUR][1000 genomes]
rs12824075	0.81[EUR][1000 genomes]
rs12825800	0.88[EUR][1000 genomes]
rs12827074	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs12828408	0.82[EUR][1000 genomes]
rs12828633	0.87[EUR][1000 genomes]
rs12829893	0.92[CEU][hapmap]
rs12829984	0.81[EUR][1000 genomes]
rs12830927	0.89[CEU][hapmap]
rs12831081	0.81[EUR][1000 genomes]
rs1399961	0.81[CEU][hapmap]
rs1515815	0.89[CEU][hapmap]
rs1969272	0.89[ASN][1000 genomes]
rs2222060	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2222061	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271660	0.81[CEU][hapmap]
rs2333838	0.81[CEU][hapmap]
rs34534928	0.81[EUR][1000 genomes]
rs35114195	0.87[EUR][1000 genomes]
rs35158437	0.87[EUR][1000 genomes]
rs35649708	0.84[EUR][1000 genomes]
rs35804181	0.80[EUR][1000 genomes]
rs35946281	0.81[EUR][1000 genomes]
rs3748269	0.85[CEU][hapmap]
rs3817309	0.82[EUR][1000 genomes]
rs4456350	0.85[CEU][hapmap]
rs4930708	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6488888	0.96[CEU][hapmap]
rs6488891	0.81[EUR][1000 genomes]
rs6488892	0.81[EUR][1000 genomes]
rs6488893	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs6488894	0.81[EUR][1000 genomes]
rs6488897	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs66471742	0.82[EUR][1000 genomes]
rs66647364	0.87[EUR][1000 genomes]
rs66690784	0.80[EUR][1000 genomes]
rs67178535	0.82[EUR][1000 genomes]
rs67516712	0.83[EUR][1000 genomes]
rs7132115	0.81[CEU][hapmap]
rs7133199	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs7133543	0.80[EUR][1000 genomes]
rs7133734	0.81[EUR][1000 genomes]
rs7134074	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs7135267	0.82[EUR][1000 genomes]
rs7135542	0.80[CEU][hapmap]
rs7135624	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7135660	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7136939	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7137946	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7138503	0.86[EUR][1000 genomes]
rs7139193	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7294984	0.93[CEU][hapmap]
rs7295552	0.84[CEU][hapmap]
rs7296804	0.82[EUR][1000 genomes]
rs7297576	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs7298440	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7298831	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs7301065	0.82[EUR][1000 genomes]
rs7301907	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302183	0.84[CEU][hapmap]
rs7302449	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302649	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7302788	0.80[EUR][1000 genomes]
rs7304837	0.81[EUR][1000 genomes]
rs7305838	0.82[EUR][1000 genomes]
rs7306549	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs7307008	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs7307343	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7308234	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7308398	0.82[CEU][hapmap]
rs7308862	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs7309528	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7310918	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7313032	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs7313140	0.87[EUR][1000 genomes]
rs7313261	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs7313628	0.89[CEU][hapmap]
rs73219037	0.81[EUR][1000 genomes]
rs7397160	0.82[EUR][1000 genomes]
rs7397745	0.84[CEU][hapmap]
rs7397930	0.80[EUR][1000 genomes]
rs7398152	0.81[EUR][1000 genomes]
rs7398298	0.82[EUR][1000 genomes]
rs7399128	0.82[CEU][hapmap]
rs7399224	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs786444	0.85[CEU][hapmap]
rs786448	0.85[CEU][hapmap]
rs7953596	0.81[EUR][1000 genomes]
rs7953599	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7958693	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs7959553	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7960951	0.86[EUR][1000 genomes]
rs7963498	0.81[EUR][1000 genomes]
rs7963968	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs7964443	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs7966867	0.92[CEU][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7968029	0.81[EUR][1000 genomes]
rs7969130	0.81[EUR][1000 genomes]
rs7969964	0.80[EUR][1000 genomes]
rs7973155	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7973695	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7974279	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs7975119	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7975233	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7978447	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7979528	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs882563	0.84[CEU][hapmap]
rs908373	0.85[CEU][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	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv832534	chr12:124157605-124234611	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2250026	TCTN2	cis	Artery Tibial	GTEx
rs2250026	DDX55	cis	Brain Pons	GTEx
rs2250026	TCTN2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124197000-124198600	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr12:124197200-124198600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
3	chr12:124197200-124198600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr12:124197200-124199000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr12:124197200-124199200	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr12:124197400-124198800	Flanking Active TSS	Fetal Brain Female	brain
7	chr12:124197400-124199000	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr12:124197400-124199000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr12:124197400-124199000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
10	chr12:124197400-124199000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr12:124197600-124198600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:124197600-124198600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr12:124197600-124198600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr12:124197600-124198600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:124197600-124198600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:124197600-124198600	Flanking Active TSS	Fetal Brain Male	brain
17	chr12:124197600-124198600	Flanking Active TSS	Fetal Heart	heart
18	chr12:124197600-124198600	Flanking Active TSS	Thymus	Thymus
19	chr12:124197600-124198800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr12:124197600-124198800	Flanking Active TSS	Colonic Mucosa	Colon
21	chr12:124197600-124198800	Flanking Active TSS	Dnd41	blood
22	chr12:124197600-124198800	Flanking Active TSS	NHEK	skin
23	chr12:124197600-124199000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:124197600-124199000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:124197600-124199000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr12:124197600-124199000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:124197600-124199000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr12:124197600-124199200	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr12:124197600-124200000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:124197600-124200400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:124197600-124234400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr12:124197800-124198600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
33	chr12:124197800-124198600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:124197800-124198600	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr12:124197800-124198600	Flanking Active TSS	Fetal Kidney	kidney
36	chr12:124197800-124198600	Flanking Active TSS	HepG2	liver
37	chr12:124197800-124198800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:124197800-124198800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr12:124197800-124198800	Enhancers	Placenta	Placenta
40	chr12:124197800-124198800	Flanking Active TSS	Hela-S3	cervix
41	chr12:124197800-124199000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:124197800-124199000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr12:124197800-124199200	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr12:124197800-124199200	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr12:124197800-124199200	Enhancers	Small Intestine	intestine
46	chr12:124197800-124199600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:124197800-124199600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr12:124197800-124202600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr12:124198000-124198600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
50	chr12:124198000-124198600	Flanking Active TSS	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links