Variant report

Variant	rs2291503
Chromosome Location	chr9:19052923-19052924
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:19049135..19050932-chr9:19052465..19054640,2	K562	blood:
2	chr9:19051025..19055237-chr9:19064013..19066512,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147874	Chromatin interaction
ENSG00000155876	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1006120	0.82[ASW][hapmap]
rs10122088	0.93[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs10757016	0.82[CHB][hapmap]
rs10757018	0.82[CHB][hapmap]
rs10757020	0.81[CHB][hapmap]
rs10757026	0.81[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12349207	0.87[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap]
rs2039011	0.86[CHB][hapmap]
rs2171956	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2184656	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs3802335	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4367642	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4395970	0.82[CHB][hapmap]
rs4977280	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4977476	0.82[CHB][hapmap]
rs4977488	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4977491	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6415731	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];0.82[LWK][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6475272	0.82[ASW][hapmap];0.82[CHB][hapmap]
rs6475273	0.82[CHB][hapmap]
rs6475303	0.80[CEU][hapmap]
rs7021907	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7025258	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7030791	0.90[CHB][hapmap]
rs7042340	0.83[EUR][1000 genomes]
rs7042382	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs7045203	0.86[CHB][hapmap]
rs7048069	0.85[EUR][1000 genomes]
rs7858618	0.84[ASW][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs7874721	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7874786	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9298798	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv973452	chr9:19033958-19053096	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2291503	PLIN2	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19050600-19056600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:19050600-19060800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:19050600-19062600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:19050600-19063600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:19050600-19069000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:19050800-19074200	Weak transcription	Lung	lung
7	chr9:19051000-19053400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr9:19051000-19056600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:19051000-19059000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr9:19051200-19057000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:19051400-19053000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr9:19051400-19053600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr9:19051400-19054400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr9:19051400-19054800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:19051400-19055400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr9:19051400-19056600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr9:19051400-19056600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:19051400-19056600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr9:19051400-19056600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:19051400-19056600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:19051400-19066400	Weak transcription	Colonic Mucosa	Colon
22	chr9:19051600-19055200	Weak transcription	Placenta	Placenta
23	chr9:19051600-19055600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr9:19051600-19055800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr9:19051600-19056400	Weak transcription	Fetal Intestine Small	intestine
26	chr9:19051600-19056400	Weak transcription	Hela-S3	cervix
27	chr9:19051600-19056600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr9:19051600-19056600	Weak transcription	Esophagus	oesophagus
29	chr9:19051600-19056600	Weak transcription	Fetal Intestine Large	intestine
30	chr9:19051600-19056600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr9:19051600-19056600	Weak transcription	Fetal Muscle Leg	muscle
32	chr9:19051600-19056600	Weak transcription	Fetal Thymus	thymus
33	chr9:19051600-19074400	Weak transcription	Spleen	Spleen
34	chr9:19051600-19101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr9:19051800-19055800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr9:19051800-19056000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:19051800-19056000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr9:19051800-19056200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr9:19051800-19056600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr9:19051800-19056600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:19051800-19056600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr9:19051800-19056800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr9:19051800-19057000	Weak transcription	A549	lung
44	chr9:19051800-19057200	Weak transcription	Brain Substantia Nigra	brain
45	chr9:19051800-19057400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr9:19051800-19059000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr9:19051800-19059400	Weak transcription	HSMMtube	muscle
48	chr9:19051800-19070200	Weak transcription	Fetal Kidney	kidney
49	chr9:19051800-19089000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr9:19052000-19053600	Enhancers	Pancreatic Islets	Pancreatic Islet

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