Variant report

Variant	rs7561070
Chromosome Location	chr2:11932173-11932174
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11931701..11933805-chr2:11935275..11937564,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1006538	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs10205312	0.93[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs10205400	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs10209969	0.83[ASN][1000 genomes]
rs13407101	0.81[ASN][1000 genomes]
rs13412852	0.89[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs1469952	0.91[ASN][1000 genomes]
rs17603420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2278513	0.89[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2358041	0.85[ASN][1000 genomes]
rs2358042	0.89[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2358126	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs2577264	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3795974	0.81[GIH][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs4076055	0.93[CHD][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap]
rs4129757	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669778	0.86[CHD][hapmap]
rs6717910	0.89[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs6757892	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72773994	0.83[ASN][1000 genomes]
rs7595221	0.89[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7607755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893342	0.84[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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS 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 miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7561070	LPIN1	cis	cerebellum	SCAN
rs7561070	LPIN1	cis	Thyroid	GTEx
rs7561070	LPIN1	cis	parietal	SCAN
rs7561070	LPIN1	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11916800-11961200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:11919400-11940400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:11919400-11943400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:11919400-11961800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:11919600-11940800	Strong transcription	Left Ventricle	heart
6	chr2:11919600-11940800	Strong transcription	NHEK	skin
7	chr2:11919600-11968400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:11919800-11933600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:11919800-11934400	Strong transcription	K562	blood
10	chr2:11919800-11937600	Strong transcription	HepG2	liver
11	chr2:11919800-11939600	Strong transcription	Fetal Thymus	thymus
12	chr2:11919800-11940000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:11919800-11940000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:11919800-11940400	Strong transcription	Dnd41	blood
15	chr2:11919800-11940600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr2:11919800-11940600	Strong transcription	Placenta	Placenta
17	chr2:11919800-11948400	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:11919800-11949000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:11919800-11957600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:11919800-11957800	Strong transcription	Primary T cells from cord blood	blood
21	chr2:11919800-11959200	Strong transcription	Liver	Liver
22	chr2:11919800-11960400	Weak transcription	Stomach Mucosa	stomach
23	chr2:11919800-11963200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr2:11919800-11967600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:11919800-11968400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:11919800-11968800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:11920000-11936800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
28	chr2:11920000-11940400	Strong transcription	HMEC	breast
29	chr2:11920000-11941000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:11920200-11934000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr2:11920200-11937200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:11920200-11939600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:11920200-11940800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:11920400-11939800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:11920400-11940400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:11920400-11940400	Strong transcription	Gastric	stomach
37	chr2:11924600-11947800	Weak transcription	Right Atrium	heart
38	chr2:11925200-11936200	Strong transcription	Adipose Nuclei	Adipose
39	chr2:11925200-11940200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr2:11925200-11941000	Strong transcription	Ovary	ovary
41	chr2:11925200-11949400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr2:11925200-11964800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:11925200-11968600	Strong transcription	NHLF	lung
44	chr2:11925400-11933800	Strong transcription	Fetal Brain Female	brain
45	chr2:11925400-11934800	Strong transcription	NHDF-Ad	bronchial
46	chr2:11925400-11936800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr2:11925400-11938800	Strong transcription	Osteobl	bone
48	chr2:11925400-11940800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr2:11925600-11932600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr2:11925600-11935400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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