Variant report

Variant	rs12030552
Chromosome Location	chr1:10096085-10096086
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9960360..9963162-chr1:10094643..10096453,2	K562	blood:
2	chr1:10092968..10095123-chr1:10095971..10097506,2	MCF-7	breast:
3	chr1:10001502..10006445-chr1:10090966..10096976,9	MCF-7	breast:
4	chr1:10001294..10005828-chr1:10093316..10096471,4	K562	blood:
5	chr1:10093957..10096871-chr1:10101261..10104242,3	K562	blood:

Variant related genes	Relation type
ENSG00000173614	Chromatin interaction
ENSG00000130939	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000228150	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10864441	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11121515	0.88[ASN][1000 genomes]
rs11121517	0.81[AFR][1000 genomes]
rs12068865	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12564842	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74051808	0.82[ASN][1000 genomes]
rs9430244	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12030552	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10092200-10096200	Active TSS	K562	blood
2	chr1:10092400-10096200	Active TSS	HMEC	breast
3	chr1:10092600-10096200	Active TSS	Hela-S3	cervix
4	chr1:10093800-10097800	Weak transcription	Spleen	Spleen
5	chr1:10094000-10097000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:10094000-10097200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:10094000-10097600	Weak transcription	Lung	lung
8	chr1:10094000-10102800	Weak transcription	Pancreas	Pancrea
9	chr1:10094000-10104200	Weak transcription	Gastric	stomach
10	chr1:10094200-10096200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:10094200-10096800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:10094600-10106000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:10094800-10097200	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:10094800-10098000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:10094800-10105000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:10094800-10105200	Weak transcription	Right Ventricle	heart
17	chr1:10094800-10105200	Weak transcription	Small Intestine	intestine
18	chr1:10094800-10106000	Weak transcription	Colonic Mucosa	Colon
19	chr1:10094800-10106200	Weak transcription	Stomach Mucosa	stomach
20	chr1:10094800-10119400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:10095000-10096200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:10095000-10096200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:10095000-10096200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:10095000-10096200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr1:10095000-10096200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:10095000-10096200	Weak transcription	Fetal Thymus	thymus
27	chr1:10095000-10096200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:10095000-10096400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:10095000-10096400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:10095000-10096400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:10095000-10096400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:10095000-10096600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:10095000-10096600	Weak transcription	Liver	Liver
34	chr1:10095000-10096600	Weak transcription	Fetal Intestine Small	intestine
35	chr1:10095000-10096600	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr1:10095000-10096800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:10095000-10096800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:10095000-10096800	Weak transcription	Osteobl	bone
39	chr1:10095000-10097200	Weak transcription	Primary T cells from cord blood	blood
40	chr1:10095000-10097200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:10095000-10097200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:10095000-10097200	Weak transcription	Brain Substantia Nigra	brain
43	chr1:10095000-10097200	Weak transcription	Fetal Intestine Large	intestine
44	chr1:10095000-10097400	Weak transcription	Adipose Nuclei	Adipose
45	chr1:10095000-10097400	Weak transcription	Colon Smooth Muscle	Colon
46	chr1:10095000-10097400	Weak transcription	Fetal Lung	lung
47	chr1:10095000-10097400	Weak transcription	NH-A	brain
48	chr1:10095000-10097600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:10095000-10097600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:10095000-10097800	Weak transcription	Primary hematopoietic stem cells	blood

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