Variant report

Variant	rs12479282
Chromosome Location	chr2:209156071-209156072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 154 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs10171006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10173938	0.94[ASN][1000 genomes]
rs10175739	0.85[CHB][hapmap];1.00[EUR][1000 genomes]
rs10176626	0.91[ASN][1000 genomes]
rs10182087	0.86[CHB][hapmap]
rs10186531	0.88[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10189031	0.91[ASN][1000 genomes]
rs10197958	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10201702	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10208004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208191	0.88[CHB][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10208295	0.88[CHB][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10210393	0.88[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10804168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10932256	0.88[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10932259	0.88[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10932260	0.91[ASN][1000 genomes]
rs11677618	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691208	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11691313	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11695873	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12185547	1.00[EUR][1000 genomes]
rs12465862	1.00[EUR][1000 genomes]
rs12478198	1.00[EUR][1000 genomes]
rs12617521	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12618837	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12621871	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12623816	0.88[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12694105	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694109	0.88[CHB][hapmap];1.00[EUR][1000 genomes]
rs13392540	0.86[CHB][hapmap]
rs1370370	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1437414	0.88[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1446320	1.00[EUR][1000 genomes]
rs1446321	1.00[EUR][1000 genomes]
rs1465803	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1465804	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1529979	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1561240	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1584200	0.94[ASN][1000 genomes]
rs1595329	0.85[CHB][hapmap]
rs16840798	0.88[CHB][hapmap]
rs16840864	0.88[CHB][hapmap]
rs16840898	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16840910	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16840936	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16841092	0.88[CHB][hapmap]
rs16841231	0.88[CHB][hapmap]
rs16841233	0.88[CHB][hapmap]
rs16841234	0.85[CHB][hapmap]
rs1838794	1.00[EUR][1000 genomes]
rs1838795	1.00[EUR][1000 genomes]
rs1838796	1.00[EUR][1000 genomes]
rs1866044	0.88[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1866045	0.88[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1898436	0.88[CHB][hapmap]
rs1900239	0.91[ASN][1000 genomes]
rs2028146	1.00[EUR][1000 genomes]
rs2043720	1.00[EUR][1000 genomes]
rs2044457	1.00[EUR][1000 genomes]
rs2118295	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2118296	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2118297	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2196604	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2304544	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2363463	1.00[EUR][1000 genomes]
rs2363465	0.88[ASN][1000 genomes]
rs2363466	0.94[ASN][1000 genomes]
rs2363468	0.88[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2363469	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2363579	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2885785	1.00[EUR][1000 genomes]
rs2885786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856350	0.88[CHB][hapmap]
rs4462735	0.88[CHB][hapmap]
rs4499359	0.95[AFR][1000 genomes]
rs4673385	1.00[EUR][1000 genomes]
rs4673386	1.00[EUR][1000 genomes]
rs4673390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4673391	0.94[ASN][1000 genomes]
rs4673392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4673393	0.91[ASN][1000 genomes]
rs4673395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4673396	0.96[AFR][1000 genomes]
rs4675745	1.00[EUR][1000 genomes]
rs4675747	1.00[EUR][1000 genomes]
rs4675748	0.88[CHB][hapmap];0.91[ASN][1000 genomes]
rs4675750	0.88[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4675751	0.88[CHB][hapmap];0.91[ASN][1000 genomes]
rs4675754	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4675755	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4675757	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4675758	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4675760	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs57553077	1.00[EUR][1000 genomes]
rs57797425	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60446438	0.93[ASN][1000 genomes]
rs6435436	1.00[EUR][1000 genomes]
rs6435437	1.00[EUR][1000 genomes]
rs6435441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6435443	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6435444	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6435445	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6435446	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6435450	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6435452	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6435454	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6705163	1.00[EUR][1000 genomes]
rs6708926	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6709286	0.92[AFR][1000 genomes]
rs6711933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6713477	0.88[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6718402	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6720289	0.87[AFR][1000 genomes]
rs6721780	0.88[CHB][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6724208	0.91[ASN][1000 genomes]
rs6725932	0.88[CHB][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6730328	0.86[AFR][1000 genomes]
rs6733607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6734963	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6736599	0.91[ASN][1000 genomes]
rs6742461	0.88[CHB][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6751982	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6758207	0.80[AMR][1000 genomes]
rs73983727	0.90[ASN][1000 genomes]
rs7564882	1.00[EUR][1000 genomes]
rs7569723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7574324	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7576852	1.00[EUR][1000 genomes]
rs7580715	1.00[EUR][1000 genomes]
rs7581075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7583022	0.88[CHB][hapmap]
rs7587752	0.91[ASN][1000 genomes]
rs7605498	1.00[EUR][1000 genomes]
rs893253	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs893255	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs893256	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9283521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9288392	0.91[ASN][1000 genomes]
rs934712	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs934714	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs959660	0.88[CHB][hapmap]
rs959855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs962595	0.88[CHB][hapmap]
rs9646839	0.88[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs976247	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs994696	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs994697	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv875752	chr2:209141066-209235373	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209136000-209171800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:209136200-209161600	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr2:209139000-209163400	Weak transcription	Right Ventricle	heart
4	chr2:209139200-209159400	Weak transcription	Small Intestine	intestine
5	chr2:209139400-209180000	Strong transcription	Fetal Thymus	thymus
6	chr2:209139800-209161800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:209141200-209180000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:209141800-209169000	Weak transcription	Hela-S3	cervix
9	chr2:209145800-209158400	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr2:209147400-209225600	Weak transcription	Stomach Mucosa	stomach
11	chr2:209147800-209168200	Weak transcription	Gastric	stomach
12	chr2:209148600-209163400	Weak transcription	Lung	lung
13	chr2:209148600-209167600	Weak transcription	Esophagus	oesophagus
14	chr2:209148600-209169600	Weak transcription	Spleen	Spleen
15	chr2:209149600-209179800	Strong transcription	Dnd41	blood
16	chr2:209150000-209156400	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr2:209150000-209158000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:209150000-209160800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:209150000-209160800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:209150200-209156200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:209150200-209156400	Strong transcription	Placenta	Placenta
22	chr2:209150400-209160800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:209150800-209157000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:209150800-209159400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:209151000-209159000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr2:209152400-209156200	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr2:209152600-209156200	Strong transcription	Brain Anterior Caudate	brain
28	chr2:209152600-209163400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:209152600-209163400	Weak transcription	Fetal Intestine Small	intestine
30	chr2:209152600-209163400	Weak transcription	NHEK	skin
31	chr2:209152800-209156200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:209152800-209156200	Strong transcription	Fetal Kidney	kidney
33	chr2:209152800-209156200	Strong transcription	A549	lung
34	chr2:209152800-209156200	Strong transcription	HMEC	breast
35	chr2:209152800-209157000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr2:209152800-209158400	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr2:209152800-209161800	Strong transcription	HSMM	muscle
38	chr2:209153000-209156200	Strong transcription	Rectal Smooth Muscle	rectum
39	chr2:209153000-209156200	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:209153000-209159000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:209153200-209165800	Weak transcription	Fetal Heart	heart
42	chr2:209153400-209159000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:209153600-209158200	ZNF genes & repeats	GM12878-XiMat	blood
44	chr2:209153800-209159000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:209153800-209161600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:209154000-209163400	Weak transcription	Left Ventricle	heart
47	chr2:209154000-209163600	Weak transcription	Colonic Mucosa	Colon
48	chr2:209154000-209168400	Weak transcription	NHLF	lung
49	chr2:209154400-209157200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:209154600-209156200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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