Variant report

Variant	rs4140809
Chromosome Location	chr7:8132006-8132007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:8008233..8010906-chr7:8131128..8133418,2	MCF-7	breast:
2	chr7:8121598..8125026-chr7:8129163..8132409,4	MCF-7	breast:
3	chr7:8123610..8126481-chr7:8130672..8132477,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106415	Chromatin interaction
ENSG00000233108	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10226050	0.83[YRI][hapmap]
rs10229643	0.83[YRI][hapmap]
rs10241457	0.81[MEX][hapmap];0.82[TSI][hapmap];0.89[YRI][hapmap]
rs10243846	0.90[YRI][hapmap]
rs10246564	0.88[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10273241	0.89[YRI][hapmap]
rs10486205	0.83[YRI][hapmap]
rs11976862	0.86[YRI][hapmap]
rs12702693	0.83[YRI][hapmap]
rs17568389	0.83[YRI][hapmap]
rs2058277	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2191321	0.93[YRI][hapmap]
rs3735457	0.88[CEU][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs37977	0.84[TSI][hapmap];0.86[YRI][hapmap]
rs37981	0.80[TSI][hapmap];0.89[YRI][hapmap]
rs37988	0.82[YRI][hapmap]
rs37994	0.91[MEX][hapmap]
rs37995	0.81[MEX][hapmap];0.80[TSI][hapmap];0.86[YRI][hapmap]
rs37997	0.82[MEX][hapmap]
rs37998	0.81[MEX][hapmap];0.89[YRI][hapmap]
rs37999	0.85[YRI][hapmap]
rs38002	0.93[YRI][hapmap]
rs38003	0.84[CEU][hapmap];0.92[YRI][hapmap]
rs38012	0.86[MEX][hapmap]
rs38013	0.91[MEX][hapmap];0.82[TSI][hapmap]
rs38014	0.83[YRI][hapmap]
rs38018	0.80[TSI][hapmap]
rs38019	0.85[YRI][hapmap]
rs4236406	0.85[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap]
rs4720761	0.81[MEX][hapmap];0.82[TSI][hapmap];0.89[YRI][hapmap]
rs4725060	0.83[YRI][hapmap]
rs4725068	0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];0.80[JPT][hapmap];0.81[LWK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9692283	0.93[YRI][hapmap]

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	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv1020686	chr7:8095118-8311985	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv538723	chr7:8095118-8311985	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv1009766	chr7:8106112-8134286	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4140809	PLA2G5	trans	cerebellum	SCAN
rs4140809	IGF1	trans	cerebellum	SCAN
rs4140809	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8067000-8135400	Weak transcription	Pancreas	Pancrea
2	chr7:8096000-8151600	Weak transcription	Spleen	Spleen
3	chr7:8103000-8135400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr7:8109000-8132800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr7:8109200-8133400	Weak transcription	Fetal Intestine Small	intestine
6	chr7:8109200-8145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:8123800-8132200	Strong transcription	Primary B cells from cord blood	blood
8	chr7:8125000-8136400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:8125400-8136800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:8126000-8133400	Weak transcription	Hela-S3	cervix
11	chr7:8126200-8133000	Weak transcription	Liver	Liver
12	chr7:8126200-8135200	Weak transcription	Fetal Stomach	stomach
13	chr7:8126200-8137200	Weak transcription	Left Ventricle	heart
14	chr7:8126400-8133800	Weak transcription	Fetal Intestine Large	intestine
15	chr7:8126400-8133800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr7:8126400-8134800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr7:8126400-8135000	Weak transcription	Thymus	Thymus
18	chr7:8126400-8135400	Weak transcription	Fetal Heart	heart
19	chr7:8126600-8132200	Weak transcription	Adipose Nuclei	Adipose
20	chr7:8127000-8132600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr7:8127000-8138000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr7:8127000-8138200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr7:8127200-8132400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr7:8127200-8134200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr7:8127200-8136200	Weak transcription	Brain Germinal Matrix	brain
26	chr7:8127600-8134200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr7:8127800-8135800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:8127800-8137400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr7:8127800-8138000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr7:8127800-8144600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr7:8128400-8136800	Weak transcription	Dnd41	blood
32	chr7:8129200-8144000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr7:8129400-8133600	Weak transcription	GM12878-XiMat	blood
34	chr7:8129400-8135000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr7:8129600-8132800	Strong transcription	Primary T cells from cord blood	blood
36	chr7:8130200-8133000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr7:8130400-8132200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr7:8130400-8133800	Weak transcription	HepG2	liver
39	chr7:8130400-8135000	Weak transcription	Fetal Thymus	thymus
40	chr7:8131600-8132800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr7:8131800-8132200	Enhancers	Right Atrium	heart
42	chr7:8131800-8132400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr7:8131800-8132800	Enhancers	HMEC	breast
44	chr7:8131800-8133000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:8132000-8132200	Enhancers	H9 Cell Line	embryonic stem cell
46	chr7:8132000-8132200	Enhancers	HSMMtube	muscle
47	chr7:8132000-8132400	Enhancers	Psoas Muscle	Psoas
48	chr7:8132000-8132400	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr7:8132000-8132600	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr7:8132000-8132800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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