Variant report

Variant	rs12080800
Chromosome Location	chr1:165845042-165845043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:165844323..165845929-chr1:165851824..165854208,2	MCF-7	breast:
2	chr1:165796218..165799498-chr1:165844441..165848225,3	K562	blood:
3	chr1:165840374..165842176-chr1:165842789..165845400,2	K562	blood:
4	chr1:165736698..165740092-chr1:165841486..165845302,4	K562	blood:
5	chr1:165822075..165824045-chr1:165844384..165846604,2	K562	blood:
6	chr1:165843122..165847161-chr1:165847770..165853662,6	K562	blood:

Variant related genes	Relation type
ENSG00000224358	Chromatin interaction
ENSG00000143183	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	0.86[EUR][1000 genomes]
rs10918297	0.85[CEU][hapmap]
rs10918301	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12125493	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];0.93[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];0.86[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];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3806333	0.86[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	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7543127	0.84[CEU][hapmap];0.93[JPT][hapmap];0.85[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
rs12080800	ITLN2	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165828000-165847200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:165828000-165849200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:165832400-165853400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:165832800-165852800	Weak transcription	Psoas Muscle	Psoas
5	chr1:165833000-165849000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:165833200-165851000	Weak transcription	Hela-S3	cervix
7	chr1:165835400-165845400	Weak transcription	Aorta	Aorta
8	chr1:165835400-165846600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:165836200-165849200	Weak transcription	Osteobl	bone
10	chr1:165840800-165851400	Weak transcription	Right Ventricle	heart
11	chr1:165840800-165851800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:165841000-165845200	Enhancers	Primary T cells from cord blood	blood
13	chr1:165841000-165847800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:165841000-165849000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:165841000-165849000	Weak transcription	HSMMtube	muscle
16	chr1:165841000-165853400	Weak transcription	Gastric	stomach
17	chr1:165842600-165845800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:165842800-165845600	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr1:165842800-165846400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:165842800-165846400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr1:165843000-165846200	Enhancers	Small Intestine	intestine
22	chr1:165843200-165845400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:165843200-165845600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:165843200-165847000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr1:165843200-165851800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:165843200-165852400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:165843400-165845200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:165843400-165845200	Enhancers	Fetal Thymus	thymus
29	chr1:165843400-165845200	Weak transcription	A549	lung
30	chr1:165843400-165845400	Enhancers	NHEK	skin
31	chr1:165843400-165845800	Enhancers	Primary hematopoietic stem cells	blood
32	chr1:165843400-165846000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:165843400-165846200	Enhancers	Stomach Mucosa	stomach
34	chr1:165843400-165846600	Weak transcription	K562	blood
35	chr1:165843400-165847200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr1:165843400-165852400	Weak transcription	NHLF	lung
37	chr1:165843600-165851200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:165843800-165845400	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr1:165843800-165845400	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr1:165843800-165845600	Enhancers	Duodenum Mucosa	Duodenum
41	chr1:165843800-165845600	Enhancers	Fetal Intestine Small	intestine
42	chr1:165843800-165845600	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr1:165843800-165846200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr1:165843800-165849800	Genic enhancers	Dnd41	blood
45	chr1:165844000-165845200	Enhancers	Pancreas	Pancrea
46	chr1:165844000-165845400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:165844000-165845600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:165844000-165845600	Enhancers	HMEC	breast
49	chr1:165844200-165846600	Weak transcription	Brain Germinal Matrix	brain
50	chr1:165844400-165845200	Enhancers	Primary B cells from peripheral blood	blood

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