Variant report

Variant	rs31248
Chromosome Location	chr5:96014683-96014684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:95995689..95998361-chr5:96013245..96014811,2	MCF-7	breast:
2	chr5:96012528..96014986-chr5:96018328..96020571,2	K562	blood:

Variant related genes	Relation type
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10045215	0.88[ASN][1000 genomes]
rs10067766	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10075736	0.88[ASN][1000 genomes]
rs1421911	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs151835	1.00[JPT][hapmap]
rs151904	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs152005	0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs152014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs152017	0.82[JPT][hapmap]
rs152020	0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2351245	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs26482	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26483	0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs26484	0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs26485	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs26503	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs26504	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs28040	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28093	0.86[JPT][hapmap]
rs28104	0.86[JPT][hapmap]
rs31249	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs31250	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4267886	0.86[ASN][1000 genomes]
rs4590196	0.95[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6556937	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6860934	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6897588	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7704167	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7705824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7733671	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs31248	CAST	cis	lung	GTEx
rs31248	CAST	cis	Whole Blood	GTEx
rs31248	CTC-506B8.1	cis	Whole Blood	GTEx
rs31248	CAST	Cis_1M	lymphoblastoid	RTeQTL
rs31248	CAST	cis	Nerve Tibial	GTEx
rs31248	CAST	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:82 , 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	chr5:95999600-96016600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:95999600-96016600	Weak transcription	HSMMtube	muscle
5	chr5:95999600-96026000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:95999600-96028200	Weak transcription	Aorta	Aorta
7	chr5:95999600-96037800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:95999600-96038000	Weak transcription	Fetal Lung	lung
9	chr5:95999800-96022800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:95999800-96024600	Weak transcription	Fetal Heart	heart
11	chr5:96000400-96016400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:96000400-96018400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:96000800-96016200	Weak transcription	NH-A	brain
14	chr5:96000800-96037600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr5:96001600-96037000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr5:96002400-96018400	Weak transcription	Psoas Muscle	Psoas
17	chr5:96002400-96027800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:96002400-96037600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr5:96002400-96038200	Weak transcription	Esophagus	oesophagus
20	chr5:96003000-96022800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:96004800-96028200	Weak transcription	Lung	lung
22	chr5:96004800-96036600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:96005000-96038000	Weak transcription	Ovary	ovary
24	chr5:96005000-96038200	Weak transcription	Gastric	stomach
25	chr5:96005600-96021400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:96005600-96027800	Weak transcription	Left Ventricle	heart
27	chr5:96007200-96016400	Weak transcription	Brain Anterior Caudate	brain
28	chr5:96007400-96016600	Weak transcription	Right Atrium	heart
29	chr5:96007400-96018200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr5:96007400-96018400	Weak transcription	Colonic Mucosa	Colon
31	chr5:96007400-96022200	Weak transcription	Right Ventricle	heart
32	chr5:96007400-96025400	Weak transcription	Pancreas	Pancrea
33	chr5:96007600-96027800	Weak transcription	Fetal Intestine Large	intestine
34	chr5:96008000-96018000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr5:96009200-96014800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr5:96009200-96037600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr5:96010600-96016000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:96010800-96015600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:96010800-96015600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr5:96010800-96016200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr5:96010800-96016400	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr5:96011000-96015800	Strong transcription	HMEC	breast
43	chr5:96011000-96017000	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr5:96011200-96016200	Strong transcription	Primary B cells from cord blood	blood
45	chr5:96011600-96015400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr5:96012000-96016400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:96012000-96016400	Weak transcription	Brain Substantia Nigra	brain
48	chr5:96012000-96026400	Weak transcription	NHLF	lung
49	chr5:96012200-96021400	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr5:96012200-96022800	Weak transcription	HUVEC	blood vessel

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