Variant report

Variant	rs12901794
Chromosome Location	chr15:35260738-35260739
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:35256436..35258004-chr15:35259347..35262190,2	MCF-7	breast:
2	chr15:35260390..35263299-chr15:35270062..35272008,3	K562	blood:
3	chr15:35252626..35258121-chr15:35259367..35263228,9	K562	blood:
4	chr15:35255428..35258097-chr15:35259367..35262801,3	K562	blood:
5	chr15:35259687..35263562-chr15:35278927..35282925,7	K562	blood:
6	chr15:35260342..35263784-chr15:35278927..35282487,7	K562	blood:
7	chr15:35219148..35220809-chr15:35259856..35261653,2	K562	blood:
8	chr15:35260390..35261999-chr15:35270459..35271963,2	K562	blood:
9	chr15:34330030..34332710-chr15:35259474..35262090,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169857	Chromatin interaction
ENSG00000021776	Chromatin interaction
ENSG00000212768	Chromatin interaction
ENSG00000198146	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10152246	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10438394	0.86[ASN][1000 genomes]
rs10444812	0.82[EUR][1000 genomes]
rs10519967	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11073076	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11629721	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11635485	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11636350	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11852957	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12439825	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12441204	0.82[ASN][1000 genomes]
rs12442905	0.87[ASN][1000 genomes]
rs12591197	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12593379	0.82[EUR][1000 genomes]
rs12593603	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12593818	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12595318	0.80[ASN][1000 genomes]
rs12708534	0.94[ASN][1000 genomes]
rs12898639	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12901028	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12901394	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901457	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12901466	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12915053	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12915493	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1376784	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2060809	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2060810	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2060811	0.95[ASN][1000 genomes]
rs2060812	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305411	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28498500	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28715915	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36067547	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816447	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4513050	0.93[ASN][1000 genomes]
rs4923817	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4923818	0.84[EUR][1000 genomes]
rs4923845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4923849	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4924344	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4924355	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4924357	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4924369	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495726	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6495728	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6495729	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6495730	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7164151	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7164169	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7164266	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7165835	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7167892	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7170280	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7172507	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7177337	0.95[ASN][1000 genomes]
rs7179205	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7179833	0.93[ASN][1000 genomes]
rs7181836	0.92[ASN][1000 genomes]
rs7182356	0.95[ASN][1000 genomes]
rs7497306	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8024212	0.82[AMR][1000 genomes]
rs8029192	0.81[AMR][1000 genomes]
rs8031861	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8037610	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs963425	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9806487	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9920236	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9920529	0.95[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	esv3350109	chr15:34668106-35534229	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv522411	chr15:34953986-35462981	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv2761865	chr15:35101678-35271639	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv832967	chr15:35110102-35267906	Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:35198800-35261200	Weak transcription	Esophagus	oesophagus
2	chr15:35221200-35260800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:35229400-35261000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:35232200-35260800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:35235000-35260800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:35235200-35260800	Weak transcription	Fetal Brain Female	brain
7	chr15:35236600-35260800	Weak transcription	Fetal Kidney	kidney
8	chr15:35240000-35261000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:35240600-35260800	Weak transcription	Brain Anterior Caudate	brain
10	chr15:35243200-35261200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr15:35244600-35260800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:35244800-35260800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:35244800-35260800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:35245000-35260800	Weak transcription	NHDF-Ad	bronchial
15	chr15:35248400-35260800	Weak transcription	Osteobl	bone
16	chr15:35252200-35261000	Weak transcription	Aorta	Aorta
17	chr15:35254600-35260800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr15:35254800-35260800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:35255600-35260800	Weak transcription	Right Ventricle	heart
20	chr15:35255600-35260800	Weak transcription	NH-A	brain
21	chr15:35256200-35260800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:35256800-35260800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:35256800-35260800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:35256800-35260800	Weak transcription	Fetal Intestine Small	intestine
25	chr15:35256800-35260800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:35257400-35260800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr15:35257400-35260800	Weak transcription	HSMMtube	muscle
28	chr15:35258200-35260800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr15:35258400-35260800	Enhancers	Liver	Liver
30	chr15:35258600-35260800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr15:35258600-35261000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr15:35258800-35260800	Enhancers	Brain Germinal Matrix	brain
33	chr15:35258800-35260800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:35259000-35260800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:35259000-35260800	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr15:35259000-35260800	Weak transcription	Brain Substantia Nigra	brain
37	chr15:35259000-35260800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr15:35259200-35260800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:35259200-35260800	Enhancers	Adipose Nuclei	Adipose
40	chr15:35259400-35260800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:35259400-35260800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:35259400-35260800	Enhancers	Brain Cingulate Gyrus	brain
43	chr15:35259400-35260800	Enhancers	Colon Smooth Muscle	Colon
44	chr15:35259400-35260800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr15:35259400-35260800	Enhancers	Stomach Smooth Muscle	stomach
46	chr15:35259400-35261000	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr15:35259600-35260800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr15:35259600-35260800	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr15:35259600-35260800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:35259600-35260800	Enhancers	Brain Angular Gyrus	brain

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