Variant report

Variant	rs12471242
Chromosome Location	chr2:208855135-208855136
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10497895	0.81[GIH][hapmap]
rs12464255	0.81[GIH][hapmap]
rs12465292	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13431014	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1452521	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17459574	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17459758	0.93[CEU][hapmap];0.90[GIH][hapmap];0.87[TSI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17537670	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17538061	0.81[GIH][hapmap]
rs28463196	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4502388	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62190863	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62190896	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62190898	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62190900	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62190904	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62190905	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62192772	0.82[AMR][1000 genomes]
rs6435402	0.93[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6740362	0.93[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72969822	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7565251	0.84[CEU][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7588162	0.87[CEU][hapmap];0.81[GIH][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs930745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv875743	chr2:208688648-208940023	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208827400-208857400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:208834000-208864000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:208834800-208865000	Weak transcription	HSMMtube	muscle
4	chr2:208835800-208855400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:208835800-208860800	Weak transcription	Small Intestine	intestine
6	chr2:208836000-208878400	Weak transcription	Fetal Kidney	kidney
7	chr2:208840000-208863800	Weak transcription	Placenta	Placenta
8	chr2:208841600-208864800	Weak transcription	HepG2	liver
9	chr2:208841600-208865200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:208841800-208864800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:208842000-208862000	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:208842000-208864200	Weak transcription	Fetal Thymus	thymus
13	chr2:208842200-208856200	Weak transcription	Brain Angular Gyrus	brain
14	chr2:208842200-208856600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:208842200-208857200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:208842200-208861800	Weak transcription	Adipose Nuclei	Adipose
17	chr2:208842200-208861800	Weak transcription	Liver	Liver
18	chr2:208842200-208862000	Weak transcription	Lung	lung
19	chr2:208842200-208862400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:208842200-208862400	Weak transcription	Left Ventricle	heart
21	chr2:208842200-208862400	Weak transcription	Ovary	ovary
22	chr2:208842200-208864200	Weak transcription	Fetal Brain Female	brain
23	chr2:208842200-208864200	Weak transcription	Fetal Lung	lung
24	chr2:208842200-208864400	Weak transcription	Brain Substantia Nigra	brain
25	chr2:208842200-208864400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:208842200-208864600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr2:208842200-208864800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:208842200-208864800	Weak transcription	Aorta	Aorta
29	chr2:208842200-208864800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:208842200-208864800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:208842200-208864800	Weak transcription	Right Ventricle	heart
32	chr2:208842200-208865000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:208842200-208866600	Weak transcription	Gastric	stomach
34	chr2:208842200-208867600	Weak transcription	Thymus	Thymus
35	chr2:208842200-208871200	Weak transcription	Esophagus	oesophagus
36	chr2:208842400-208856800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:208842400-208861000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:208842400-208864200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr2:208842400-208864400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr2:208842400-208864800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:208842400-208866000	Weak transcription	Brain Germinal Matrix	brain
42	chr2:208842400-208867200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr2:208842400-208868200	Weak transcription	Dnd41	blood
44	chr2:208842600-208864000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:208842800-208862400	Weak transcription	Fetal Stomach	stomach
46	chr2:208843400-208861800	Weak transcription	Right Atrium	heart
47	chr2:208843600-208871200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:208845200-208859600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:208845400-208856400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:208848600-208859000	Weak transcription	Monocytes-CD14+_RO01746	blood

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