Variant report

Variant	rs12088598
Chromosome Location	chr1:9980865-9980866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9971162..9973726-chr1:9979028..9981341,2	MCF-7	breast:
2	chr1:9979462..9981194-chr1:9999339..10001219,2	K562	blood:
3	chr1:9979666..9982180-chr1:9989888..9991989,2	K562	blood:
4	chr1:9970359..9972833-chr1:9979234..9983583,5	K562	blood:

Variant related genes	Relation type
ENSG00000178585	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11121501	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11121509	0.95[AMR][1000 genomes]
rs12058979	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12059092	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12060375	0.91[AMR][1000 genomes]
rs12062953	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12064822	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12065908	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070725	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12071307	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12082318	0.95[AMR][1000 genomes]
rs12086598	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12094254	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12097182	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289478	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297843	0.98[AMR][1000 genomes]
rs4845912	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846104	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57702810	0.87[ASN][1000 genomes]
rs60132751	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61743470	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6663059	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664208	0.91[AMR][1000 genomes]
rs7516611	0.93[AMR][1000 genomes]
rs7535945	0.95[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv545380	chr1:9918183-9987007	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	nsv534854	chr1:9964726-10001012	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12088598	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9971200-9981800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:9971400-9982600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:9971400-9987400	Weak transcription	Fetal Stomach	stomach
4	chr1:9971400-9993600	Weak transcription	Aorta	Aorta
5	chr1:9971400-10002000	Weak transcription	Small Intestine	intestine
6	chr1:9971600-9988600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:9971600-9991200	Weak transcription	NHEK	skin
8	chr1:9971800-9985600	Weak transcription	Primary T cells from cord blood	blood
9	chr1:9971800-9986600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:9971800-9987000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:9971800-9987600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:9971800-9989000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:9971800-9991800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:9972600-9982400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:9972600-9988000	Weak transcription	Lung	lung
16	chr1:9972600-9988600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr1:9972600-10002200	Weak transcription	Right Atrium	heart
18	chr1:9972800-9989600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:9973000-9988400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:9975000-9982200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:9975200-10002600	Weak transcription	Stomach Mucosa	stomach
22	chr1:9977000-9982200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:9977000-9991800	Weak transcription	Brain Germinal Matrix	brain
24	chr1:9977200-9982000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:9977200-9982200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:9977400-9982200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:9978200-9990200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:9978600-9984800	Weak transcription	HepG2	liver
29	chr1:9980200-9988400	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:9980400-9990200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:9980600-9981000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:9980800-9981000	Enhancers	Left Ventricle	heart
33	chr1:9980800-9983800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr1:9980800-9988600	Weak transcription	Rectal Mucosa Donor 29	rectum

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