Variant report

Variant	rs4027384
Chromosome Location	chr14:64467070-64467071
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	chr14:64459939..64462358-chr14:64466934..64469220,2	MCF-7	breast:
2	chr14:64319797..64321605-chr14:64466270..64468504,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11624124	0.83[EUR][1000 genomes]
rs11844554	0.86[EUR][1000 genomes]
rs11850427	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1255855	0.85[EUR][1000 genomes]
rs1255858	0.88[EUR][1000 genomes]
rs1255859	0.88[EUR][1000 genomes]
rs1255860	0.88[EUR][1000 genomes]
rs1255861	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1255862	0.92[EUR][1000 genomes]
rs1255863	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1255864	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1255865	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255866	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255868	0.85[EUR][1000 genomes]
rs1255870	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1255886	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255889	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255893	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1255894	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1255895	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1255897	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255898	0.81[EUR][1000 genomes]
rs1255899	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255904	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1255906	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255907	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255909	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1255911	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255912	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1262234	0.87[EUR][1000 genomes]
rs1262236	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1273193	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2275019	0.87[EUR][1000 genomes]
rs2775000	0.88[EUR][1000 genomes]
rs2775001	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2775004	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2781426	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2781427	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2792207	0.88[EUR][1000 genomes]
rs2884113	0.87[EUR][1000 genomes]
rs4027383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7142401	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7156778	0.88[EUR][1000 genomes]
rs7159878	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7161272	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8010312	0.84[CEU][hapmap]
rs8022079	0.83[EUR][1000 genomes]
rs8022635	0.90[EUR][1000 genomes]
rs945025	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs945029	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs946916	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1038825	chr14:64109441-64491720	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv456326	chr14:64420413-64754361	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv564905	chr14:64420413-64754361	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv902020	chr14:64434288-64506541	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4027384	C14orf39	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64395000-64491000	Weak transcription	Psoas Muscle	Psoas
2	chr14:64419200-64489000	Weak transcription	Small Intestine	intestine
3	chr14:64435200-64471800	Weak transcription	Hela-S3	cervix
4	chr14:64439800-64467800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr14:64440800-64480400	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr14:64441600-64467600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr14:64442400-64491000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr14:64452400-64480600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr14:64452600-64479200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr14:64456600-64468200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr14:64457000-64470600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr14:64457000-64474600	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr14:64457000-64480000	Strong transcription	Dnd41	blood
14	chr14:64457000-64502000	Strong transcription	Placenta	Placenta
15	chr14:64457000-64519200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr14:64457200-64470600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr14:64457200-64476000	Strong transcription	Fetal Brain Female	brain
18	chr14:64457200-64480200	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr14:64457600-64467800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr14:64458200-64468000	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr14:64458800-64490400	Weak transcription	Colonic Mucosa	Colon
22	chr14:64459000-64468400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr14:64459400-64467400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
24	chr14:64459600-64471000	Weak transcription	Esophagus	oesophagus
25	chr14:64459600-64478800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr14:64459600-64481200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr14:64460000-64481200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr14:64460000-64488000	Weak transcription	Pancreas	Pancrea
29	chr14:64460000-64513400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr14:64460600-64495000	Weak transcription	NHDF-Ad	bronchial
31	chr14:64461000-64470400	Weak transcription	Aorta	Aorta
32	chr14:64461400-64472200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr14:64461800-64472000	Strong transcription	Left Ventricle	heart
34	chr14:64462000-64468800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr14:64462200-64469200	Strong transcription	Fetal Muscle Leg	muscle
36	chr14:64462200-64472400	Strong transcription	Primary T cells from cord blood	blood
37	chr14:64462200-64473000	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr14:64462400-64469000	Strong transcription	Fetal Kidney	kidney
39	chr14:64462600-64472200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr14:64462600-64472200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr14:64462600-64475800	Strong transcription	Fetal Intestine Large	intestine
42	chr14:64462600-64479000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr14:64462600-64479000	Strong transcription	Fetal Stomach	stomach
44	chr14:64462800-64467400	Weak transcription	HSMM	muscle
45	chr14:64462800-64470600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr14:64462800-64470600	Strong transcription	Ovary	ovary
47	chr14:64462800-64472000	Strong transcription	Adipose Nuclei	Adipose
48	chr14:64462800-64472000	Strong transcription	GM12878-XiMat	blood
49	chr14:64462800-64472400	Strong transcription	Fetal Lung	lung
50	chr14:64462800-64472800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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