Variant report

Variant	rs12369680
Chromosome Location	chr12:41729419-41729420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10506191	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10506192	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs10735995	0.96[CEU][hapmap]
rs10785235	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10785258	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs10785259	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10785261	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10785262	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10785263	0.96[CEU][hapmap]
rs10785264	1.00[CEU][hapmap]
rs10880054	1.00[CEU][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10880063	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880067	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs10880071	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11180770	0.80[JPT][hapmap]
rs11180834	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11180836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11180843	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11180851	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11180863	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs11180864	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs11180878	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11614231	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11835941	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap]
rs12146801	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12370984	0.85[EUR][1000 genomes]
rs12422274	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12578784	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12817575	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1405549	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1405552	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1458176	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs1527090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1534279	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1534280	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1544000	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1902907	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1902909	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1902911	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1918221	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1918226	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1918227	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2199030	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2405911	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2733289	0.84[JPT][hapmap]
rs2897268	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34220247	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34892771	0.85[EUR][1000 genomes]
rs6582332	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6582334	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6582336	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7133365	1.00[CEU][hapmap]
rs7301366	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7315276	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7488531	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7954106	1.00[CEU][hapmap]
rs7956320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7957823	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7960955	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7963312	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs7966732	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs7967532	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7979586	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs930905	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs961337	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9783512	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832383	chr12:41693298-41846934	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41721200-41729600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:41722800-41733000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:41723200-41731200	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:41726800-41730400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:41727000-41730200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:41727000-41730600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:41727000-41730600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr12:41727600-41730400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr12:41727600-41730400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr12:41727800-41730200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:41728000-41730400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:41728400-41729800	Weak transcription	Brain Angular Gyrus	brain
13	chr12:41728600-41729600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:41728600-41729800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:41728600-41729800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:41728600-41729800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:41728600-41729800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr12:41728600-41729800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:41728600-41729800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:41728600-41730000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:41728600-41730000	Weak transcription	Brain Anterior Caudate	brain
22	chr12:41728600-41730000	Weak transcription	Brain Substantia Nigra	brain
23	chr12:41728800-41729800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:41728800-41729800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:41728800-41729800	Weak transcription	Brain Germinal Matrix	brain
26	chr12:41729400-41732800	Weak transcription	Stomach Smooth Muscle	stomach

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