Variant report

Variant	rs12888212
Chromosome Location	chr14:66200458-66200459
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	chr14:66198099..66200739-chr14:66200960..66203371,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10483785	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1075566	0.86[EUR][1000 genomes]
rs11158601	0.80[EUR][1000 genomes]
rs11158611	0.87[EUR][1000 genomes]
rs11622271	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11622829	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11624045	0.83[EUR][1000 genomes]
rs11624104	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11625362	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11625882	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11627067	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11627184	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11627185	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11627578	0.87[EUR][1000 genomes]
rs11627605	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11628765	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11628840	0.87[EUR][1000 genomes]
rs12050182	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12050231	0.87[EUR][1000 genomes]
rs12586842	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12588838	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12879805	0.81[EUR][1000 genomes]
rs12882200	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12883382	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12886334	0.82[EUR][1000 genomes]
rs12887673	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12887957	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12889002	0.82[EUR][1000 genomes]
rs12890902	0.88[EUR][1000 genomes]
rs12894034	0.87[EUR][1000 genomes]
rs12894466	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12894902	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12896663	0.83[EUR][1000 genomes]
rs1535173	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1958561	0.81[EUR][1000 genomes]
rs1998036	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2064694	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2268961	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2268962	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2300865	0.89[EUR][1000 genomes]
rs2411351	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2411355	0.81[EUR][1000 genomes]
rs2411357	0.80[EUR][1000 genomes]
rs2411404	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2411405	0.87[EUR][1000 genomes]
rs3783709	0.81[EUR][1000 genomes]
rs4581615	0.81[EUR][1000 genomes]
rs4902415	0.87[EUR][1000 genomes]
rs4902416	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6573624	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6573626	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67957534	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7142018	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7142165	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7142219	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7142651	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7146829	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7149301	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7157449	0.86[EUR][1000 genomes]
rs7161123	0.81[EUR][1000 genomes]
rs730807	0.86[EUR][1000 genomes]
rs743084	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs743085	0.81[EUR][1000 genomes]
rs7493004	0.90[EUR][1000 genomes]
rs761831	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8005710	0.81[EUR][1000 genomes]
rs8010876	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8012278	0.81[EUR][1000 genomes]
rs8018278	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8022764	0.83[AMR][1000 genomes]
rs927004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv1036403	chr14:65724229-66208114	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv1043943	chr14:65782466-66698411	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
3	nsv542120	chr14:65782466-66698411	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
4	nsv1039168	chr14:65811750-66308343	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
5	esv3366524	chr14:65924360-66423862	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1045000	chr14:66010886-66372518	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1042671	chr14:66010886-66399888	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:66179000-66206200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr14:66185400-66209000	Weak transcription	Brain Angular Gyrus	brain
3	chr14:66186400-66208800	Weak transcription	Fetal Brain Female	brain
4	chr14:66187000-66209000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr14:66187400-66208600	Weak transcription	Placenta	Placenta
6	chr14:66188000-66210800	Weak transcription	Fetal Lung	lung
7	chr14:66188200-66201400	Weak transcription	Psoas Muscle	Psoas
8	chr14:66188400-66210600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr14:66188800-66208800	Weak transcription	Liver	Liver
10	chr14:66189000-66209000	Weak transcription	NHDF-Ad	bronchial
11	chr14:66189600-66210800	Weak transcription	NHLF	lung
12	chr14:66189800-66209000	Weak transcription	HSMMtube	muscle
13	chr14:66190000-66208800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr14:66190000-66210800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr14:66190200-66210800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr14:66190400-66217000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr14:66191600-66212000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr14:66191800-66200800	Weak transcription	Brain Anterior Caudate	brain
19	chr14:66191800-66204400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr14:66191800-66208600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr14:66191800-66208800	Weak transcription	Gastric	stomach
22	chr14:66191800-66208800	Weak transcription	Pancreas	Pancrea
23	chr14:66191800-66210800	Weak transcription	HSMM	muscle
24	chr14:66191800-66217800	Weak transcription	Small Intestine	intestine
25	chr14:66192000-66206800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr14:66192200-66208800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr14:66192400-66210200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr14:66192600-66210400	Weak transcription	Right Ventricle	heart
29	chr14:66192800-66210600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr14:66192800-66211800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr14:66192800-66212200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr14:66193000-66218800	Weak transcription	Colonic Mucosa	Colon
33	chr14:66193200-66206600	Strong transcription	Dnd41	blood
34	chr14:66193200-66208800	Weak transcription	Adipose Nuclei	Adipose
35	chr14:66193800-66208800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr14:66193800-66208800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr14:66194200-66207400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr14:66194200-66208800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr14:66194200-66210600	Weak transcription	Spleen	Spleen
40	chr14:66194400-66201000	Weak transcription	Brain Germinal Matrix	brain
41	chr14:66194400-66201400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr14:66194400-66201400	Weak transcription	Left Ventricle	heart
43	chr14:66194400-66204400	Weak transcription	Fetal Intestine Large	intestine
44	chr14:66194400-66205400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr14:66194400-66208600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr14:66194400-66208600	Weak transcription	Ovary	ovary
47	chr14:66194400-66208800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr14:66194400-66208800	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr14:66194400-66208800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr14:66194400-66208800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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