Variant report

Variant	rs246109
Chromosome Location	chr5:96010474-96010475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96008651..96011619-chr5:96011622..96013374,2	MCF-7	breast:
2	chr5:96001062..96004442-chr5:96008712..96011350,3	MCF-7	breast:
3	chr5:95997430..95999756-chr5:96010396..96013026,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10067766	0.84[ASN][1000 genomes]
rs1421911	0.84[ASN][1000 genomes]
rs152017	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6860934	0.81[ASN][1000 genomes]
rs6897588	0.84[ASN][1000 genomes]
rs7704167	0.81[ASN][1000 genomes]
rs7705824	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs246109	CAST	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95999400-96018200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:95999400-96038000	Weak transcription	Fetal Stomach	stomach
3	chr5:95999600-96012400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:95999600-96016600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:95999600-96016600	Weak transcription	HSMMtube	muscle
6	chr5:95999600-96026000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:95999600-96028200	Weak transcription	Aorta	Aorta
8	chr5:95999600-96037800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:95999600-96038000	Weak transcription	Fetal Lung	lung
10	chr5:95999800-96010800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr5:95999800-96022800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr5:95999800-96024600	Weak transcription	Fetal Heart	heart
13	chr5:96000400-96010800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:96000400-96013400	Weak transcription	Placenta	Placenta
15	chr5:96000400-96016400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:96000400-96018400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:96000600-96010800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:96000600-96011000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr5:96000600-96013200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:96000800-96010800	Weak transcription	Osteobl	bone
21	chr5:96000800-96011000	Weak transcription	HUVEC	blood vessel
22	chr5:96000800-96011800	Weak transcription	Primary T cells from cord blood	blood
23	chr5:96000800-96013000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:96000800-96016200	Weak transcription	NH-A	brain
25	chr5:96000800-96037600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr5:96001000-96011000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr5:96001000-96011000	Weak transcription	HMEC	breast
28	chr5:96001200-96011600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr5:96001400-96010800	Weak transcription	NHDF-Ad	bronchial
30	chr5:96001400-96013000	Weak transcription	NHEK	skin
31	chr5:96001400-96013200	Weak transcription	HSMM	muscle
32	chr5:96001600-96037000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr5:96002200-96011000	Weak transcription	NHLF	lung
34	chr5:96002400-96010800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:96002400-96012800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr5:96002400-96018400	Weak transcription	Psoas Muscle	Psoas
37	chr5:96002400-96027800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr5:96002400-96037600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr5:96002400-96038200	Weak transcription	Esophagus	oesophagus
40	chr5:96002600-96010800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr5:96003000-96022800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr5:96003200-96013200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr5:96004600-96012200	Weak transcription	Thymus	Thymus
44	chr5:96004800-96011600	Weak transcription	A549	lung
45	chr5:96004800-96028200	Weak transcription	Lung	lung
46	chr5:96004800-96036600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr5:96005000-96010800	Weak transcription	Small Intestine	intestine
48	chr5:96005000-96038000	Weak transcription	Ovary	ovary
49	chr5:96005000-96038200	Weak transcription	Gastric	stomach
50	chr5:96005400-96010800	Weak transcription	Hela-S3	cervix

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