Variant report

Variant	rs1996879
Chromosome Location	chr12:39205600-39205601
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ALG10B-8	chr12:39204585-39205690	ucscGeneNc_uc001rmj_1

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10160990	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095573	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1095578	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169105	0.84[AFR][1000 genomes]
rs11169268	0.82[EUR][1000 genomes]
rs11169604	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169615	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169618	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11537523	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11559976	0.84[AFR][1000 genomes]
rs1356267	0.88[EUR][1000 genomes]
rs1400281	0.92[EUR][1000 genomes]
rs1486343	0.84[AFR][1000 genomes]
rs1516553	0.81[EUR][1000 genomes]
rs1516557	0.83[EUR][1000 genomes]
rs1523119	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1533917	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1533918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1607040	0.90[EUR][1000 genomes]
rs1615648	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1621487	0.86[EUR][1000 genomes]
rs1684426	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1719833	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1719847	0.86[EUR][1000 genomes]
rs1719860	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1914052	0.88[EUR][1000 genomes]
rs2056529	0.92[EUR][1000 genomes]
rs2069210	0.82[EUR][1000 genomes]
rs2455609	0.84[AFR][1000 genomes]
rs2630782	0.84[AFR][1000 genomes]
rs2653754	0.84[AFR][1000 genomes]
rs2653761	0.82[AFR][1000 genomes]
rs2730946	0.84[AFR][1000 genomes]
rs2730955	0.84[AFR][1000 genomes]
rs2730957	0.84[AFR][1000 genomes]
rs4002228	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4768394	0.92[EUR][1000 genomes]
rs56091726	0.88[AFR][1000 genomes]
rs56310820	0.88[AFR][1000 genomes]
rs7136317	0.88[AFR][1000 genomes]
rs7298168	0.92[EUR][1000 genomes]
rs73269131	0.84[AFR][1000 genomes]
rs74086007	0.88[AFR][1000 genomes]
rs7974247	0.90[EUR][1000 genomes]
rs7978838	0.88[EUR][1000 genomes]
rs826839	0.84[AFR][1000 genomes]
rs826841	0.84[AFR][1000 genomes]
rs826845	0.89[EUR][1000 genomes]
rs826847	0.89[EUR][1000 genomes]
rs826849	0.95[EUR][1000 genomes]
rs826853	0.82[EUR][1000 genomes]
rs826854	0.80[EUR][1000 genomes]
rs826857	0.82[EUR][1000 genomes]
rs826861	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs826862	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs826867	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs826868	0.84[EUR][1000 genomes]
rs826869	0.82[EUR][1000 genomes]
rs826871	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs826872	0.82[EUR][1000 genomes]
rs826882	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs826884	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs826885	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs826890	0.84[AFR][1000 genomes]
rs851933	0.82[EUR][1000 genomes]
rs862331	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs862332	0.96[EUR][1000 genomes]
rs866120	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv676	chr12:39184359-39215822	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS	lncRNA	n/a	inside rSNPs	diseases
2	nsv1047623	chr12:39187817-39539939	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39184200-39205800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:39201200-39208000	Weak transcription	A549	lung
3	chr12:39201600-39208800	Weak transcription	Esophagus	oesophagus
4	chr12:39201800-39205600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr12:39201800-39216600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:39203200-39213400	Weak transcription	Pancreas	Pancrea
7	chr12:39203200-39220200	Weak transcription	Psoas Muscle	Psoas
8	chr12:39203200-39276000	Weak transcription	Aorta	Aorta
9	chr12:39203400-39205800	Weak transcription	Liver	Liver
10	chr12:39203600-39216800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:39203800-39205800	Weak transcription	Ovary	ovary
12	chr12:39204000-39205600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:39204000-39205600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr12:39204000-39205600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:39204000-39206000	Strong transcription	Primary hematopoietic stem cells	blood
16	chr12:39204000-39284800	Weak transcription	Lung	lung
17	chr12:39204200-39205800	Weak transcription	Left Ventricle	heart
18	chr12:39204200-39213400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:39204200-39216800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:39204400-39209400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:39204600-39205800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:39204600-39205800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:39204800-39207200	Strong transcription	Stomach Smooth Muscle	stomach
24	chr12:39204800-39228800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:39204800-39231800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr12:39205000-39206200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:39205000-39217000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:39205200-39205600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:39205400-39205600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
30	chr12:39205400-39206800	ZNF genes & repeats	GM12878-XiMat	blood
31	chr12:39205600-39205800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
32	chr12:39205600-39206200	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr12:39205600-39206200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:39205600-39206800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:39205600-39206800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:39205600-39206800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:39205600-39206800	ZNF genes & repeats	Adipose Nuclei	Adipose
38	chr12:39205600-39207200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
39	chr12:39205600-39223200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:39205600-39229400	Weak transcription	HMEC	breast

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