Variant report

Variant	rs12744387
Chromosome Location	chr1:10040509-10040510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10779735	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11121508	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12026401	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12128632	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12128636	0.82[AFR][1000 genomes]
rs1220398	0.83[AFR][1000 genomes]
rs1220422	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1237370	0.86[AFR][1000 genomes]
rs2380188	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3013785	0.81[AFR][1000 genomes]
rs4073852	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs41280780	0.88[ASN][1000 genomes]
rs61782860	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61785621	0.90[AFR][1000 genomes]
rs6541074	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6663108	0.83[AFR][1000 genomes]
rs6673580	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6683452	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72859517	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7522568	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7534615	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9943169	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12744387	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10011000-10044800	Weak transcription	NHDF-Ad	bronchial
2	chr1:10011800-10042200	Weak transcription	K562	blood
3	chr1:10016400-10042400	Weak transcription	HMEC	breast
4	chr1:10021400-10043200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:10021600-10041600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:10021600-10041600	Weak transcription	HSMMtube	muscle
7	chr1:10021600-10049000	Weak transcription	HSMM	muscle
8	chr1:10023400-10044000	Weak transcription	HepG2	liver
9	chr1:10025800-10046800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:10028400-10050000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:10029600-10041000	Weak transcription	Osteobl	bone
12	chr1:10029600-10042200	Weak transcription	GM12878-XiMat	blood
13	chr1:10030400-10041000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:10030400-10043000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:10030800-10044600	Weak transcription	Brain Germinal Matrix	brain
16	chr1:10031200-10042200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:10031200-10042200	Weak transcription	Small Intestine	intestine
18	chr1:10031600-10044600	Strong transcription	Fetal Intestine Large	intestine
19	chr1:10031600-10045600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:10031600-10046200	Strong transcription	Fetal Intestine Small	intestine
21	chr1:10031600-10047200	Strong transcription	Fetal Stomach	stomach
22	chr1:10032000-10043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:10032000-10045200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr1:10032000-10046600	Strong transcription	Liver	Liver
25	chr1:10032200-10044200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:10032200-10044200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:10032200-10045400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:10032400-10042200	Weak transcription	NH-A	brain
29	chr1:10032400-10044200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:10032600-10043400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:10032600-10044400	Strong transcription	Primary T cells from cord blood	blood
32	chr1:10032800-10057000	Weak transcription	Psoas Muscle	Psoas
33	chr1:10033800-10044600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr1:10034200-10041200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:10034200-10042200	Weak transcription	Dnd41	blood
36	chr1:10034400-10042800	Strong transcription	Placenta	Placenta
37	chr1:10034400-10048000	Weak transcription	Stomach Mucosa	stomach
38	chr1:10034600-10042200	Weak transcription	Aorta	Aorta
39	chr1:10034800-10042800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:10035600-10051800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:10036000-10042200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:10036000-10044600	Weak transcription	Fetal Kidney	kidney
43	chr1:10036000-10050400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr1:10036200-10041200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:10036200-10041200	Weak transcription	Fetal Lung	lung
46	chr1:10036200-10041600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:10036200-10042200	Weak transcription	NHLF	lung
48	chr1:10036200-10042400	Weak transcription	Brain Substantia Nigra	brain
49	chr1:10036600-10041000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr1:10036600-10041600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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