Variant report

Variant	rs12562047
Chromosome Location	chr1:165829156-165829157
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:165795539..165799937-chr1:165823038..165829386,11	MCF-7	breast:
2	chr1:165826311..165829287-chr1:165838167..165840920,2	K562	blood:
3	chr1:165819266..165822080-chr1:165829077..165831771,2	MCF-7	breast:
4	chr1:165824047..165827978-chr1:165829041..165832736,3	K562	blood:
5	chr1:165828614..165831006-chr1:165847927..165850420,2	K562	blood:

Variant related genes	Relation type
ENSG00000143183	Chromatin interaction
ENSG00000143179	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10159235	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10494448	0.89[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10918297	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12121204	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16851949	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2225980	0.97[GIH][hapmap];0.90[YRI][hapmap]
rs4657486	0.84[JPT][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs61802911	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[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	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	esv2830094	chr1:165785503-165840411	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
3	esv2755529	chr1:165813862-165858354	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv437246	chr1:165822891-165860813	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12562047	ITLN2	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165818000-165829200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:165821000-165832200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:165821800-165829400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:165823600-165831200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr1:165823600-165833000	Weak transcription	Hela-S3	cervix
6	chr1:165823600-165834000	Weak transcription	Aorta	Aorta
7	chr1:165823600-165834600	Weak transcription	Fetal Stomach	stomach
8	chr1:165823800-165829200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:165823800-165829400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:165823800-165838000	Weak transcription	Fetal Lung	lung
11	chr1:165823800-165840200	Weak transcription	HUVEC	blood vessel
12	chr1:165824800-165829200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:165824800-165829400	Enhancers	Fetal Thymus	thymus
14	chr1:165824800-165830000	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr1:165825000-165829400	Enhancers	Thymus	Thymus
16	chr1:165825000-165829800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:165825200-165831000	Weak transcription	Brain Germinal Matrix	brain
18	chr1:165825400-165829200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:165825400-165831200	Enhancers	Fetal Intestine Large	intestine
20	chr1:165825400-165839800	Weak transcription	Primary B cells from cord blood	blood
21	chr1:165825600-165831200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:165825600-165837800	Weak transcription	Fetal Brain Female	brain
23	chr1:165825800-165831400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:165826000-165829600	Enhancers	Liver	Liver
25	chr1:165826200-165829400	Enhancers	Left Ventricle	heart
26	chr1:165826200-165829400	Enhancers	Stomach Mucosa	stomach
27	chr1:165826200-165831200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:165826400-165829200	Enhancers	Right Ventricle	heart
29	chr1:165826400-165829400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:165826400-165829600	Enhancers	Gastric	stomach
31	chr1:165826400-165829600	Enhancers	Pancreas	Pancrea
32	chr1:165826400-165831000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:165826400-165835000	Genic enhancers	Dnd41	blood
34	chr1:165826600-165829400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:165826600-165831200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:165826600-165831200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:165826600-165840600	Weak transcription	NH-A	brain
38	chr1:165826800-165829200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr1:165826800-165829200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:165826800-165831200	Weak transcription	Brain Substantia Nigra	brain
41	chr1:165827000-165829600	Enhancers	HSMM	muscle
42	chr1:165827000-165829600	Enhancers	HSMMtube	muscle
43	chr1:165827000-165834200	Weak transcription	Osteobl	bone
44	chr1:165827200-165831200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr1:165827400-165829200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:165827400-165829200	Active TSS	Rectal Smooth Muscle	rectum
47	chr1:165827600-165831200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:165827600-165831200	Weak transcription	GM12878-XiMat	blood
49	chr1:165827600-165831400	Weak transcription	Brain Angular Gyrus	brain
50	chr1:165827800-165831000	Weak transcription	H9 Cell Line	embryonic stem cell

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