Variant report

Variant	rs12590172
Chromosome Location	chr14:39893535-39893536
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39892960..39898062-chr14:39898504..39901618,10	MCF-7	breast:
2	chr14:39891521..39896514-chr14:39899849..39902823,6	K562	blood:

Variant related genes	Relation type
ENSG00000165355	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10133417	0.81[JPT][hapmap]
rs10137352	0.81[JPT][hapmap]
rs10137905	0.82[CHB][hapmap]
rs10162550	0.80[JPT][hapmap]
rs11157058	0.80[JPT][hapmap]
rs11157067	0.86[AFR][1000 genomes]
rs11620695	0.81[JPT][hapmap]
rs11627580	0.81[JPT][hapmap]
rs11847057	0.93[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12232110	0.93[ASN][1000 genomes]
rs12434140	0.87[CHB][hapmap]
rs12587625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12587713	0.81[JPT][hapmap]
rs12588110	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12588175	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12588483	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12589427	0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12880644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12882250	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12883652	0.87[ASN][1000 genomes]
rs12884747	0.95[AFR][1000 genomes]
rs12886769	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12894855	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12896502	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12897960	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1594842	0.80[JPT][hapmap]
rs17109073	0.80[JPT][hapmap]
rs17109296	0.83[CHB][hapmap]
rs17109300	0.82[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs17109328	0.94[AFR][1000 genomes]
rs1950329	0.95[AFR][1000 genomes]
rs1950334	0.93[AFR][1000 genomes]
rs1950336	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1950338	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1955718	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1955729	0.83[CHB][hapmap]
rs2038278	0.87[ASN][1000 genomes]
rs2057137	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2057138	0.82[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs2207291	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274396	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs2415549	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2415550	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2899888	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2899889	0.93[ASN][1000 genomes]
rs34432449	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34649642	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34687394	0.95[AFR][1000 genomes]
rs34894621	0.82[AMR][1000 genomes]
rs34928332	0.80[ASN][1000 genomes]
rs35115885	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35459433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35553183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35643160	0.95[AFR][1000 genomes]
rs35693868	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35876588	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35923045	0.94[AFR][1000 genomes]
rs36010374	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3814860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4899245	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4899277	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4899278	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4899291	0.94[AFR][1000 genomes]
rs4902528	0.87[CHB][hapmap]
rs4902569	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4902570	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4902598	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902599	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902622	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4902636	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902637	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902648	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902665	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902676	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4902692	0.82[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs56046902	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56375627	0.80[AMR][1000 genomes]
rs67439322	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs67963654	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs71407788	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71407789	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7140983	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7145821	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7148150	0.81[JPT][hapmap]
rs7148377	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7152341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7152935	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7153413	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7158709	0.95[AFR][1000 genomes]
rs7161403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718364	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs719455	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs72675487	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8003397	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8003621	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8004716	0.81[JPT][hapmap]
rs8006123	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8006321	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8020250	0.94[AFR][1000 genomes]
rs910370	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs910371	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9332387	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	39 gene(s)	inside rSNPs	diseases
3	esv3523177	chr14:39875036-40128325	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3523178	chr14:39875036-40128325	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39864600-39898800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr14:39865000-39898200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr14:39869000-39895600	Weak transcription	Hela-S3	cervix
4	chr14:39882200-39895400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr14:39886000-39895600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr14:39886200-39895600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr14:39886400-39895600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr14:39886600-39894000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr14:39886600-39894400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr14:39886600-39895600	Weak transcription	Fetal Lung	lung
11	chr14:39886600-39895800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr14:39886600-39895800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr14:39886600-39898000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr14:39886600-39900000	Weak transcription	Esophagus	oesophagus
15	chr14:39886600-39900000	Weak transcription	Pancreas	Pancrea
16	chr14:39886800-39895600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr14:39886800-39895600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr14:39886800-39895600	Weak transcription	HepG2	liver
19	chr14:39886800-39895800	Weak transcription	Brain Anterior Caudate	brain
20	chr14:39886800-39895800	Weak transcription	Fetal Thymus	thymus
21	chr14:39886800-39895800	Weak transcription	Thymus	Thymus
22	chr14:39886800-39899200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr14:39886800-39899600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr14:39887000-39895800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr14:39887000-39899200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:39887200-39895400	Weak transcription	Dnd41	blood
27	chr14:39887200-39895600	Weak transcription	GM12878-XiMat	blood
28	chr14:39887600-39898000	Weak transcription	Fetal Stomach	stomach
29	chr14:39889400-39895600	Weak transcription	Liver	Liver
30	chr14:39889600-39898800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr14:39889800-39895400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr14:39889800-39898800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr14:39890200-39895600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr14:39890200-39895600	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr14:39890200-39896800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr14:39890400-39895800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr14:39890600-39897800	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr14:39890600-39897800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr14:39890600-39897800	Weak transcription	Fetal Brain Female	brain
40	chr14:39890800-39895400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr14:39890800-39895600	Weak transcription	Primary T cells from cord blood	blood
42	chr14:39890800-39895600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr14:39890800-39895800	Weak transcription	Primary B cells from cord blood	blood
44	chr14:39890800-39895800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr14:39890800-39896400	Enhancers	Fetal Heart	heart
46	chr14:39891000-39895400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr14:39891000-39898400	Weak transcription	Fetal Kidney	kidney
48	chr14:39891200-39895800	Weak transcription	Fetal Muscle Leg	muscle
49	chr14:39891200-39897600	Weak transcription	Fetal Brain Male	brain
50	chr14:39891200-39898800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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