Variant report

Variant	rs2349108
Chromosome Location	chr1:165846707-165846708
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	chr1:165796218..165799498-chr1:165844441..165848225,3	K562	blood:
4	chr1:165796218..165798368-chr1:165845682..165848225,4	K562	blood:
5	chr1:165842995..165844503-chr1:165845607..165847939,2	MCF-7	breast:
6	chr1:165843122..165847161-chr1:165847770..165853662,6	K562	blood:
7	chr1:165796694..165798989-chr1:165846477..165848096,2	MCF-7	breast:

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

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1061771	1.00[ASN][1000 genomes]
rs10918307	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12090859	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2153261	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2153262	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2185267	0.89[AMR][1000 genomes]
rs2275432	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2349109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748701	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3790656	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3790657	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3790658	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3790660	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3790661	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3790662	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3790663	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3790664	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3790666	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3790667	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3790673	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3806331	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3806332	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs577133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6666697	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6681761	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6693108	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73031470	1.00[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

No data

Chromatin state (count:64 , 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	chr1:165836200-165849200	Weak transcription	Osteobl	bone
8	chr1:165840800-165851400	Weak transcription	Right Ventricle	heart
9	chr1:165840800-165851800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:165841000-165847800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:165841000-165849000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:165841000-165849000	Weak transcription	HSMMtube	muscle
13	chr1:165841000-165853400	Weak transcription	Gastric	stomach
14	chr1:165843200-165847000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr1:165843200-165851800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:165843200-165852400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:165843400-165847200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr1:165843400-165852400	Weak transcription	NHLF	lung
19	chr1:165843600-165851200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:165843800-165849800	Genic enhancers	Dnd41	blood
21	chr1:165844800-165851200	Weak transcription	Left Ventricle	heart
22	chr1:165844800-165852400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:165844800-165852400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:165845000-165848000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:165845000-165849400	Weak transcription	Brain Anterior Caudate	brain
26	chr1:165845200-165847000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr1:165845200-165848600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:165845200-165849600	Weak transcription	Pancreas	Pancrea
29	chr1:165845200-165860000	Weak transcription	Fetal Thymus	thymus
30	chr1:165845400-165847400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
31	chr1:165845400-165848200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:165845400-165850600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:165845400-165851800	Weak transcription	NHEK	skin
34	chr1:165845600-165847000	Enhancers	GM12878-XiMat	blood
35	chr1:165845600-165847600	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:165845600-165848000	Weak transcription	Fetal Heart	heart
37	chr1:165845600-165848800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:165845600-165851800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:165845600-165854000	Weak transcription	Fetal Intestine Large	intestine
40	chr1:165845600-165854000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:165845600-165861600	Weak transcription	Thymus	Thymus
42	chr1:165845800-165848000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:165845800-165848800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:165846000-165847000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
45	chr1:165846000-165848400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
46	chr1:165846000-165848600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:165846000-165848600	Strong transcription	HSMM	muscle
48	chr1:165846000-165849200	Weak transcription	HepG2	liver
49	chr1:165846200-165847000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
50	chr1:165846200-165847000	Weak transcription	Small Intestine	intestine

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