Variant report

Variant	rs12082318
Chromosome Location	chr1:10036009-10036010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11121501	0.93[AMR][1000 genomes]
rs11121509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12058979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12059092	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12060375	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12062953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12064822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12065908	1.00[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12070725	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12071307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12086598	0.93[AMR][1000 genomes]
rs12088598	0.95[AMR][1000 genomes]
rs12094254	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12097182	1.00[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs17034440	1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[AMR][1000 genomes]
rs2289478	0.93[AMR][1000 genomes]
rs2297843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4845912	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4846104	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4846108	0.95[AMR][1000 genomes]
rs4846187	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs60132751	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs61743470	0.93[AMR][1000 genomes]
rs6663059	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6664208	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516611	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7535945	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	nsv1005461	chr1:9972921-10038862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
9	nsv534855	chr1:9972921-10038862	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12082318	LZIC	cis	lymphoblastoid	seeQTL
rs12082318	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10010800-10036400	Weak transcription	Esophagus	oesophagus
2	chr1:10011000-10044800	Weak transcription	NHDF-Ad	bronchial
3	chr1:10011800-10042200	Weak transcription	K562	blood
4	chr1:10016400-10042400	Weak transcription	HMEC	breast
5	chr1:10019800-10037600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:10021400-10039200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:10021400-10043200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:10021600-10041600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:10021600-10041600	Weak transcription	HSMMtube	muscle
10	chr1:10021600-10049000	Weak transcription	HSMM	muscle
11	chr1:10021800-10037600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:10023400-10044000	Weak transcription	HepG2	liver
13	chr1:10025800-10046800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:10028400-10050000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:10029600-10041000	Weak transcription	Osteobl	bone
16	chr1:10029600-10042200	Weak transcription	GM12878-XiMat	blood
17	chr1:10030400-10041000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:10030400-10043000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:10030800-10044600	Weak transcription	Brain Germinal Matrix	brain
20	chr1:10031200-10037000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:10031200-10042200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:10031200-10042200	Weak transcription	Small Intestine	intestine
23	chr1:10031600-10038400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:10031600-10039000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr1:10031600-10039600	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:10031600-10044600	Strong transcription	Fetal Intestine Large	intestine
27	chr1:10031600-10045600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:10031600-10046200	Strong transcription	Fetal Intestine Small	intestine
29	chr1:10031600-10047200	Strong transcription	Fetal Stomach	stomach
30	chr1:10031800-10037000	Strong transcription	Left Ventricle	heart
31	chr1:10031800-10039000	Strong transcription	Lung	lung
32	chr1:10031800-10039200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:10031800-10039600	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:10032000-10036200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:10032000-10036200	Strong transcription	Primary B cells from cord blood	blood
36	chr1:10032000-10036600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:10032000-10036600	Strong transcription	Spleen	Spleen
38	chr1:10032000-10036800	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr1:10032000-10038000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:10032000-10038400	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr1:10032000-10039200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:10032000-10039400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr1:10032000-10039600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr1:10032000-10039600	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:10032000-10039800	Strong transcription	Fetal Muscle Leg	muscle
46	chr1:10032000-10043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:10032000-10045200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr1:10032000-10046600	Strong transcription	Liver	Liver
49	chr1:10032200-10036600	Strong transcription	Primary B cells from peripheral blood	blood
50	chr1:10032200-10036600	Strong transcription	Duodenum Smooth Muscle	Duodenum

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