Variant report

Variant	rs6876015
Chromosome Location	chr5:95163957-95163958
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	chr5:95162262..95164257-chr5:95169999..95171533,2	MCF-7	breast:
2	chr5:95156277..95158130-chr5:95161683..95164482,2	K562	blood:

Variant related genes	Relation type
ENSG00000251000	Chromatin interaction
ENSG00000173221	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11135436	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11745044	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11747430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61289286	0.96[ASN][1000 genomes]
rs61377269	0.98[ASN][1000 genomes]
rs6871404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv462255	chr5:95142817-95168155	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv598961	chr5:95142817-95168155	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv882389	chr5:95144952-95173887	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6876015	LNPEP	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95158800-95164800	Enhancers	Fetal Intestine Large	intestine
2	chr5:95159800-95164800	Enhancers	Fetal Intestine Small	intestine
3	chr5:95159800-95169800	Weak transcription	Fetal Kidney	kidney
4	chr5:95160200-95164800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr5:95160200-95169800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:95160600-95168800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:95160600-95170000	Weak transcription	Right Atrium	heart
8	chr5:95160600-95170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:95160800-95166400	Weak transcription	Gastric	stomach
10	chr5:95160800-95168000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:95160800-95168200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:95160800-95168800	Weak transcription	Placenta	Placenta
13	chr5:95160800-95169000	Weak transcription	Psoas Muscle	Psoas
14	chr5:95160800-95169800	Weak transcription	Fetal Heart	heart
15	chr5:95160800-95169800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr5:95161400-95168400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr5:95161600-95171400	Weak transcription	Small Intestine	intestine
18	chr5:95161800-95164400	Weak transcription	Pancreas	Pancrea
19	chr5:95161800-95165000	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr5:95161800-95165200	Weak transcription	Colon Smooth Muscle	Colon
21	chr5:95161800-95168000	Weak transcription	GM12878-XiMat	blood
22	chr5:95161800-95168800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:95161800-95169800	Weak transcription	Thymus	Thymus
24	chr5:95161800-95170000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:95162000-95168000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr5:95162000-95168200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:95162200-95164000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr5:95162400-95164600	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr5:95162400-95168000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr5:95162400-95169600	Weak transcription	Hela-S3	cervix
31	chr5:95162600-95164400	Enhancers	Primary B cells from cord blood	blood
32	chr5:95162800-95164200	Enhancers	Stomach Mucosa	stomach
33	chr5:95162800-95164400	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr5:95162800-95164400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr5:95162800-95164800	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr5:95163000-95164200	Enhancers	A549	lung
37	chr5:95163000-95164400	Enhancers	Liver	Liver
38	chr5:95163000-95164800	Enhancers	Lung	lung
39	chr5:95163200-95164000	Enhancers	Primary T cells from cord blood	blood
40	chr5:95163200-95164600	Enhancers	Fetal Thymus	thymus
41	chr5:95163400-95164800	Enhancers	Colonic Mucosa	Colon
42	chr5:95163400-95164800	Enhancers	HepG2	liver
43	chr5:95163600-95164000	Enhancers	Dnd41	blood
44	chr5:95163600-95164000	Flanking Active TSS	K562	blood
45	chr5:95163600-95168000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr5:95163800-95164200	Enhancers	Spleen	Spleen
47	chr5:95163800-95164400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:95163800-95164400	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr5:95163800-95164600	Enhancers	Duodenum Mucosa	Duodenum

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