Variant report

Variant	rs11892871
Chromosome Location	chr2:11878723-11878724
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11878418..11879254-chr2:11919121..11919879,2	MCF-7	breast:
2	chr2:11878641..11879395-chr2:11919018..11919604,3	K562	blood:
3	chr2:11875528..11877148-chr2:11877418..11878938,2	MCF-7	breast:
4	chr2:11878332..11879441-chr2:11918884..11919993,17	MCF-7	breast:
5	chr2:11850515..11852161-chr2:11877592..11880491,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1036393	1.00[ASN][1000 genomes]
rs11538448	1.00[ASN][1000 genomes]
rs11675463	1.00[ASN][1000 genomes]
rs11676175	1.00[ASN][1000 genomes]
rs11677240	1.00[ASN][1000 genomes]
rs11683719	1.00[ASN][1000 genomes]
rs11890442	1.00[ASN][1000 genomes]
rs11894146	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894751	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13421972	1.00[ASN][1000 genomes]
rs1561010	1.00[ASN][1000 genomes]
rs1561011	1.00[ASN][1000 genomes]
rs16857679	1.00[ASN][1000 genomes]
rs34592059	1.00[ASN][1000 genomes]
rs34928762	1.00[ASN][1000 genomes]
rs45509591	1.00[ASN][1000 genomes]
rs55890755	1.00[ASN][1000 genomes]
rs56788115	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57097271	1.00[ASN][1000 genomes]
rs59085046	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59208217	1.00[ASN][1000 genomes]
rs59408163	1.00[ASN][1000 genomes]
rs60662456	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61239977	1.00[ASN][1000 genomes]
rs61585887	0.84[EUR][1000 genomes]
rs62113260	1.00[ASN][1000 genomes]
rs62113263	1.00[ASN][1000 genomes]
rs62113264	1.00[ASN][1000 genomes]
rs62113265	1.00[ASN][1000 genomes]
rs62113266	1.00[ASN][1000 genomes]
rs62113267	1.00[ASN][1000 genomes]
rs62113293	1.00[ASN][1000 genomes]
rs62113296	1.00[ASN][1000 genomes]
rs62113297	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62113298	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62113299	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62113300	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62113302	1.00[ASN][1000 genomes]
rs62113303	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62113305	1.00[ASN][1000 genomes]
rs62113307	1.00[ASN][1000 genomes]
rs62113308	1.00[ASN][1000 genomes]
rs62113309	1.00[ASN][1000 genomes]
rs62113310	1.00[ASN][1000 genomes]
rs62113313	1.00[ASN][1000 genomes]
rs62113354	1.00[ASN][1000 genomes]
rs62113357	1.00[ASN][1000 genomes]
rs62114961	1.00[ASN][1000 genomes]
rs62114962	1.00[ASN][1000 genomes]
rs62114963	1.00[ASN][1000 genomes]
rs62114964	1.00[ASN][1000 genomes]
rs62114967	1.00[ASN][1000 genomes]
rs62114968	1.00[ASN][1000 genomes]
rs62116185	1.00[ASN][1000 genomes]
rs62116208	1.00[ASN][1000 genomes]
rs62116209	1.00[ASN][1000 genomes]
rs6707885	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716999	1.00[ASN][1000 genomes]
rs6717771	1.00[ASN][1000 genomes]
rs6726960	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6744695	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6744803	1.00[ASN][1000 genomes]
rs71446421	1.00[ASN][1000 genomes]
rs72773987	1.00[ASN][1000 genomes]
rs72773997	1.00[ASN][1000 genomes]
rs72773999	1.00[ASN][1000 genomes]
rs72774000	1.00[ASN][1000 genomes]
rs7566112	1.00[ASN][1000 genomes]
rs7566488	1.00[ASN][1000 genomes]
rs7569901	1.00[CHD][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs7570139	1.00[ASN][1000 genomes]
rs7575000	1.00[ASN][1000 genomes]
rs7593837	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv580973	chr2:11864946-11898931	Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv580974	chr2:11867841-11898931	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11892871	LPIN1	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11874800-11878800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr2:11875000-11878800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:11875200-11883000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:11877000-11882800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:11877000-11883400	Weak transcription	Right Atrium	heart
6	chr2:11878400-11879200	Enhancers	Right Ventricle	heart
7	chr2:11878400-11879400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:11878400-11879600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:11878400-11880000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:11878600-11878800	Enhancers	Colonic Mucosa	Colon
11	chr2:11878600-11878800	Enhancers	Fetal Intestine Small	intestine
12	chr2:11878600-11878800	Enhancers	Fetal Thymus	thymus
13	chr2:11878600-11878800	Enhancers	HepG2	liver
14	chr2:11878600-11878800	Enhancers	K562	blood
15	chr2:11878600-11879000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:11878600-11879000	Enhancers	Primary B cells from peripheral blood	blood
17	chr2:11878600-11879000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr2:11878600-11879000	Enhancers	Brain Cingulate Gyrus	brain
19	chr2:11878600-11879000	Enhancers	Rectal Smooth Muscle	rectum
20	chr2:11878600-11879000	Bivalent Enhancer	GM12878-XiMat	blood
21	chr2:11878600-11879200	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr2:11878600-11879200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr2:11878600-11879200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:11878600-11879200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:11878600-11879200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:11878600-11879200	Enhancers	Ovary	ovary
27	chr2:11878600-11879200	Enhancers	Psoas Muscle	Psoas
28	chr2:11878600-11879200	Enhancers	Stomach Mucosa	stomach
29	chr2:11878600-11879200	Flanking Active TSS	Hela-S3	cervix
30	chr2:11878600-11879400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr2:11878600-11879400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:11878600-11879400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:11878600-11879400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:11878600-11879400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:11878600-11879400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:11878600-11879400	Enhancers	HMEC	breast
37	chr2:11878600-11879600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr2:11878600-11879600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:11878600-11879600	Enhancers	Liver	Liver
40	chr2:11878600-11879600	Enhancers	Placenta	Placenta
41	chr2:11878600-11879600	Enhancers	A549	lung
42	chr2:11878600-11879600	Enhancers	Osteobl	bone
43	chr2:11878600-11879800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:11878600-11879800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:11878600-11879800	Enhancers	Muscle Satellite Cultured Cells	--
46	chr2:11878600-11879800	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr2:11878600-11879800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr2:11878600-11879800	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr2:11878600-11879800	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr2:11878600-11879800	Enhancers	NHLF	lung

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