Variant report

Variant	rs2060840
Chromosome Location	chr12:44998350-44998351
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1037433	0.80[CHB][hapmap];0.94[EUR][1000 genomes]
rs1037434	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10506256	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs10748400	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10785509	0.85[CHB][hapmap]
rs10785511	0.86[CHB][hapmap]
rs10785515	0.86[EUR][1000 genomes]
rs10880653	0.85[CHB][hapmap]
rs10880654	0.86[CHB][hapmap]
rs10880655	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10880657	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10880658	0.83[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10880659	0.82[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880666	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs11182559	0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11182636	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs12815257	0.94[EUR][1000 genomes]
rs1563043	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1869162	0.83[JPT][hapmap];0.94[EUR][1000 genomes]
rs1869253	0.89[CHB][hapmap]
rs1966855	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2084843	0.92[EUR][1000 genomes]
rs2305448	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4544065	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs4768066	1.00[CEU][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768563	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768564	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs605722	1.00[CEU][hapmap];0.80[CHB][hapmap];0.83[EUR][1000 genomes]
rs678663	0.83[EUR][1000 genomes]
rs728065	0.85[CHB][hapmap]
rs7295999	0.94[EUR][1000 genomes]
rs7308509	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs7314643	0.92[EUR][1000 genomes]
rs765769	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7958389	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7968076	0.83[EUR][1000 genomes]
rs7970849	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs838973	0.81[EUR][1000 genomes]
rs966383	0.80[CHB][hapmap];0.86[EUR][1000 genomes]
rs978540	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv2762976	chr12:44969431-45000228	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44940200-44999600	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr12:44943400-44998600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr12:44966800-45000600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr12:44977400-44998800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr12:44986600-45006600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:44986800-45015800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:44990400-45004800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:44992000-44999400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:44992200-45006400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:44993000-45006800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:44994400-45004200	Weak transcription	Brain Germinal Matrix	brain
12	chr12:44995800-45001400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:44995800-45003000	Weak transcription	Fetal Brain Female	brain
14	chr12:44996800-44998400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr12:44997000-44999400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr12:44997800-44998600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:44997800-44998600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:44998000-45005600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:44998200-45024400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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