Variant report

Variant	rs12076922
Chromosome Location	chr1:10165301-10165302
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11121516	0.85[AFR][1000 genomes]
rs12070814	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12092513	0.81[JPT][hapmap]
rs17034545	0.81[JPT][hapmap]
rs17034558	0.81[JPT][hapmap]
rs17034560	0.81[JPT][hapmap]
rs3762290	0.95[GIH][hapmap]
rs4543799	0.95[GIH][hapmap]
rs60085278	0.95[ASN][1000 genomes]
rs60208411	0.91[ASN][1000 genomes]
rs6659436	0.81[JPT][hapmap]
rs6671289	0.81[GIH][hapmap]
rs6673887	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6685910	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6687550	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6700518	0.81[JPT][hapmap]
rs74051807	0.84[ASN][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	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
2	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv522629	chr1:10125765-10239197	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv522525	chr1:10165301-10165316	Strong transcription Weak transcription Genic enhancers Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12076922	LZIC	Cis_1M	lymphoblastoid	RTeQTL
rs12076922	LZIC	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10107400-10165400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:10125800-10165400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:10125800-10165400	Weak transcription	Fetal Brain Male	brain
4	chr1:10126400-10165400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:10132600-10165400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:10134600-10166200	Weak transcription	Colonic Mucosa	Colon
7	chr1:10134600-10166600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:10135200-10165400	Weak transcription	HUVEC	blood vessel
9	chr1:10137600-10165600	Weak transcription	Esophagus	oesophagus
10	chr1:10144000-10165400	Weak transcription	HSMMtube	muscle
11	chr1:10145400-10189600	Weak transcription	Psoas Muscle	Psoas
12	chr1:10145600-10165400	Weak transcription	Brain Angular Gyrus	brain
13	chr1:10145600-10165400	Weak transcription	Fetal Heart	heart
14	chr1:10145800-10165400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:10145800-10197000	Weak transcription	Stomach Mucosa	stomach
16	chr1:10153800-10172200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:10154800-10172000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:10154800-10183000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:10155000-10171400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr1:10155200-10166400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:10156400-10165400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:10156800-10165400	Weak transcription	Spleen	Spleen
23	chr1:10157200-10165600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:10157800-10165400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:10158400-10178000	Strong transcription	Primary T cells from cord blood	blood
26	chr1:10158600-10174000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:10160200-10175800	Strong transcription	Fetal Stomach	stomach
28	chr1:10160400-10167600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:10160400-10167800	Strong transcription	Fetal Muscle Leg	muscle
30	chr1:10160400-10168000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:10160400-10169600	Strong transcription	Dnd41	blood
32	chr1:10160400-10171400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:10160600-10167000	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:10160600-10171800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:10160800-10165600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:10160800-10167200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr1:10160800-10168600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:10161000-10165400	Strong transcription	Adipose Nuclei	Adipose
39	chr1:10161000-10165400	Strong transcription	Stomach Smooth Muscle	stomach
40	chr1:10161000-10167000	Strong transcription	A549	lung
41	chr1:10161000-10167200	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr1:10161000-10167400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:10161000-10167400	Strong transcription	NHDF-Ad	bronchial
44	chr1:10161000-10167600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:10161000-10167600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:10161000-10168000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:10161000-10169000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:10161000-10169200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:10161000-10169200	Strong transcription	K562	blood
50	chr1:10161000-10169400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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