Variant report

Variant	rs12125493
Chromosome Location	chr1:165847489-165847490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:165737635..165740279-chr1:165846111..165848320,2	MCF-7	breast:
2	chr1:165845971..165849103-chr1:165855397..165857265,3	MCF-7	breast:
3	chr1:165847454..165850029-chr1:165851841..165853502,3	K562	blood:
4	chr1:165796218..165799498-chr1:165844441..165848225,3	K562	blood:
5	chr1:165796218..165798368-chr1:165845682..165848225,4	K562	blood:
6	chr1:165842995..165844503-chr1:165845607..165847939,2	MCF-7	breast:
7	chr1:165796694..165798989-chr1:165846477..165848096,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143183	Chromatin interaction
ENSG00000224358	Chromatin interaction
ENSG00000143179	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10800165	0.85[EUR][1000 genomes]
rs10918297	0.85[CEU][hapmap]
rs10918301	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12080800	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2225980	0.96[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3762365	0.92[CEU][hapmap];0.80[CHB][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3790659	0.88[CEU][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3806333	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4657486	0.88[CEU][hapmap];0.94[GIH][hapmap];0.83[EUR][1000 genomes]
rs485338	0.85[TSI][hapmap]
rs495529	0.83[CHD][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs536109	0.81[CEU][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.85[ASN][1000 genomes]
rs544617	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs7519919	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7543127	0.84[CEU][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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
rs12125493	ITLN2	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165828000-165849200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:165832400-165853400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:165832800-165852800	Weak transcription	Psoas Muscle	Psoas
4	chr1:165833000-165849000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:165833200-165851000	Weak transcription	Hela-S3	cervix
6	chr1:165836200-165849200	Weak transcription	Osteobl	bone
7	chr1:165840800-165851400	Weak transcription	Right Ventricle	heart
8	chr1:165840800-165851800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:165841000-165847800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:165841000-165849000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:165841000-165849000	Weak transcription	HSMMtube	muscle
12	chr1:165841000-165853400	Weak transcription	Gastric	stomach
13	chr1:165843200-165851800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:165843200-165852400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:165843400-165852400	Weak transcription	NHLF	lung
16	chr1:165843600-165851200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:165843800-165849800	Genic enhancers	Dnd41	blood
18	chr1:165844800-165851200	Weak transcription	Left Ventricle	heart
19	chr1:165844800-165852400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:165844800-165852400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:165845000-165848000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:165845000-165849400	Weak transcription	Brain Anterior Caudate	brain
23	chr1:165845200-165848600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:165845200-165849600	Weak transcription	Pancreas	Pancrea
25	chr1:165845200-165860000	Weak transcription	Fetal Thymus	thymus
26	chr1:165845400-165848200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:165845400-165850600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:165845400-165851800	Weak transcription	NHEK	skin
29	chr1:165845600-165847600	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:165845600-165848000	Weak transcription	Fetal Heart	heart
31	chr1:165845600-165848800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:165845600-165851800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:165845600-165854000	Weak transcription	Fetal Intestine Large	intestine
34	chr1:165845600-165854000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:165845600-165861600	Weak transcription	Thymus	Thymus
36	chr1:165845800-165848000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:165845800-165848800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:165846000-165848400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
39	chr1:165846000-165848600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:165846000-165848600	Strong transcription	HSMM	muscle
41	chr1:165846000-165849200	Weak transcription	HepG2	liver
42	chr1:165846200-165848200	ZNF genes & repeats	A549	lung
43	chr1:165846200-165849000	Weak transcription	Liver	Liver
44	chr1:165846200-165849000	Weak transcription	Stomach Mucosa	stomach
45	chr1:165846400-165853600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:165846600-165847600	ZNF genes & repeats	Brain Germinal Matrix	brain
47	chr1:165846600-165848000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
48	chr1:165846600-165848200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr1:165846600-165848200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
50	chr1:165846800-165850600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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