Variant report

Variant	rs12828039
Chromosome Location	chr12:45099395-45099396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10506253	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs10506254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs10506255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10785516	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10880662	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10880663	0.87[EUR][1000 genomes]
rs11182607	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11182608	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11182617	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11182622	0.89[EUR][1000 genomes]
rs11182633	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs11609932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11615822	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12578861	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12579312	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12580824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12581256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12812313	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12812412	0.85[JPT][hapmap]
rs12817968	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12818520	0.84[JPT][hapmap]
rs12820225	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12825403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12827088	0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs12827992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12830054	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12830788	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1450538	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1452259	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1452260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1452261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1517205	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][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]
rs1562965	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1597808	0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17571851	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17572194	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17573326	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17573382	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17574950	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17575124	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17575145	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17651444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17651576	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17652016	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17652045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17652213	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17652890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs1869161	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2122530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290353	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290354	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290355	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs33995718	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34059115	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34354933	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34500282	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34560815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34775637	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34882841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34985115	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35051815	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35180883	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35889925	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35934410	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35977363	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36054479	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4362200	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55841784	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55985078	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs55996511	0.93[ASN][1000 genomes]
rs57004692	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57933837	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59379685	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61932363	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61932405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66572050	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7295695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7308333	0.98[EUR][1000 genomes]
rs73098383	0.87[EUR][1000 genomes]
rs7953273	0.88[EUR][1000 genomes]
rs7971322	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7971937	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7978549	1.00[CEU][hapmap];0.99[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	nsv1049818	chr12:44486312-45133783	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3378050	chr12:44963059-45264289	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv832394	chr12:45077573-45269305	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv1049080	chr12:45097564-45195295	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45065000-45116000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:45080800-45136000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:45081400-45115600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr12:45081600-45106800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:45081800-45103000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr12:45083200-45110000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:45085400-45101000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:45085400-45105800	Weak transcription	Fetal Brain Female	brain
9	chr12:45088000-45110800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:45089000-45114200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:45089600-45106400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:45090600-45110200	Weak transcription	Brain Germinal Matrix	brain
13	chr12:45091200-45110800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:45093200-45099800	Weak transcription	Fetal Brain Male	brain
15	chr12:45094000-45102200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr12:45097400-45101000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr12:45097600-45102600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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