Variant report

Variant	rs8017888
Chromosome Location	chr14:31815374-31815375
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	chr14:31675418..31678639-chr14:31811864..31816181,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000092148	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10872851	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11156666	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11156667	0.82[CEU][hapmap]
rs11156670	0.85[ASN][1000 genomes]
rs11624447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11627106	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11627355	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12147258	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12588420	0.96[CEU][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs12886573	0.81[CHB][hapmap]
rs12893465	0.81[ASW][hapmap];0.81[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs17097870	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1888576	0.81[CEU][hapmap];0.91[GIH][hapmap];0.80[TSI][hapmap]
rs2378865	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs34709766	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35904795	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs45490191	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4981092	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4981835	0.82[AMR][1000 genomes]
rs4981842	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56314035	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6571416	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7144879	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7149240	1.00[CEU][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7150262	0.92[CEU][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs7152230	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7157977	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7159731	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7161558	0.87[MEX][hapmap]
rs8005942	0.80[EUR][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	esv2830427	chr14:31639110-32000034	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1050597	chr14:31711248-31904761	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv901589	chr14:31768231-31944723	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv3356815	chr14:31812826-31815374	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8017888	CHI3L2	trans	lymphoblastoid	seeQTL
rs8017888	C14orf126	Cis_1M	lymphoblastoid	RTeQTL
rs8017888	RP11-176H8.1	cis	Muscle Skeletal	GTEx
rs8017888	HEATR5A	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31771000-31888800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr14:31772400-31825200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr14:31782200-31875200	Weak transcription	Gastric	stomach
4	chr14:31782400-31827000	Weak transcription	Aorta	Aorta
5	chr14:31799600-31827000	Weak transcription	Right Ventricle	heart
6	chr14:31799800-31815600	Weak transcription	Colonic Mucosa	Colon
7	chr14:31799800-31829600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr14:31799800-31866800	Weak transcription	Esophagus	oesophagus
9	chr14:31800200-31839800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr14:31800400-31838200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr14:31801200-31823400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr14:31801200-31883800	Weak transcription	Small Intestine	intestine
13	chr14:31801400-31862800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr14:31801400-31875600	Weak transcription	Brain Germinal Matrix	brain
15	chr14:31801600-31824000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr14:31801600-31872400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr14:31801800-31824400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr14:31801800-31862600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr14:31802400-31825000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr14:31802400-31827200	Weak transcription	Brain Substantia Nigra	brain
21	chr14:31802400-31842800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr14:31802600-31825000	Weak transcription	GM12878-XiMat	blood
23	chr14:31802800-31872000	Weak transcription	Fetal Brain Male	brain
24	chr14:31803400-31817600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr14:31803600-31825000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr14:31803600-31833000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr14:31803600-31872600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr14:31803800-31843600	Weak transcription	A549	lung
29	chr14:31803800-31852200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr14:31804000-31825000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr14:31805600-31816400	Weak transcription	Fetal Stomach	stomach
32	chr14:31805600-31825000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr14:31805600-31851800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:31806000-31819600	Strong transcription	HSMM	muscle
35	chr14:31806200-31850800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr14:31806400-31825400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr14:31806400-31829200	Strong transcription	Placenta	Placenta
38	chr14:31806600-31826600	Weak transcription	NHEK	skin
39	chr14:31806600-31826800	Weak transcription	Hela-S3	cervix
40	chr14:31807000-31815800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr14:31807400-31825400	Weak transcription	Psoas Muscle	Psoas
42	chr14:31808000-31872600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr14:31808600-31827000	Weak transcription	Lung	lung
44	chr14:31808800-31818200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr14:31809600-31824600	Weak transcription	Pancreas	Pancrea
46	chr14:31809600-31872000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr14:31810200-31816000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr14:31810200-31822200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr14:31810200-31827800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr14:31810400-31823200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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