Variant report

Variant	rs4899368
Chromosome Location	chr14:71208996-71208997
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10129307	0.81[CEU][hapmap];0.88[AMR][1000 genomes]
rs1034769	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10873241	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873242	0.85[ASN][1000 genomes]
rs12589737	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12879569	0.87[ASW][hapmap];0.81[GIH][hapmap];0.81[LWK][hapmap];0.82[AFR][1000 genomes]
rs1476609	0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1476610	0.87[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2023955	0.83[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.81[MKK][hapmap]
rs2107665	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs2107666	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2158526	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2158527	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2332455	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2332458	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3814872	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4141095	0.87[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4899367	0.81[MKK][hapmap]
rs4899369	0.92[ASN][1000 genomes]
rs4902844	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4902852	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902863	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs6573978	0.87[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.84[TSI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6573980	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7140653	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7152246	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs7152516	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7155910	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs8006424	0.81[MKK][hapmap]
rs8007131	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8011047	0.86[GIH][hapmap]
rs8011507	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs8018294	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4899368	DPF3	cis	cerebellum	SCAN
rs4899368	FAM71D	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71185800-71219200	Weak transcription	Stomach Mucosa	stomach
2	chr14:71186000-71221600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:71186000-71221600	Weak transcription	Hela-S3	cervix
4	chr14:71189800-71209400	Strong transcription	Fetal Brain Female	brain
5	chr14:71190000-71214400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr14:71191400-71220000	Weak transcription	Fetal Brain Male	brain
7	chr14:71191600-71220200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr14:71192400-71220200	Weak transcription	Fetal Kidney	kidney
9	chr14:71192600-71221800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr14:71193400-71211400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr14:71193600-71210200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr14:71193800-71209400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr14:71193800-71209400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr14:71194000-71222000	Weak transcription	HSMMtube	muscle
15	chr14:71194200-71209600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr14:71194400-71210400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr14:71194400-71213400	Weak transcription	Psoas Muscle	Psoas
18	chr14:71194400-71221600	Weak transcription	Left Ventricle	heart
19	chr14:71194600-71218600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr14:71194600-71221600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr14:71195600-71209400	Strong transcription	Placenta	Placenta
22	chr14:71195600-71209600	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr14:71195600-71210000	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr14:71196200-71209200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr14:71196200-71217000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr14:71196400-71209400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr14:71197000-71228800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr14:71197600-71217000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr14:71198400-71209400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr14:71198400-71223400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr14:71198800-71210000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr14:71199000-71212400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr14:71199400-71209000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr14:71199600-71209400	Strong transcription	HMEC	breast
35	chr14:71199600-71219600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr14:71200000-71210200	Strong transcription	NHEK	skin
37	chr14:71200200-71216400	Weak transcription	Brain Hippocampus Middle	brain
38	chr14:71200400-71215400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr14:71200600-71224200	Weak transcription	Spleen	Spleen
40	chr14:71200800-71213000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr14:71201200-71215200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr14:71201200-71228000	Weak transcription	Colonic Mucosa	Colon
43	chr14:71201600-71219000	Weak transcription	Lung	lung
44	chr14:71201600-71220600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr14:71202600-71210000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr14:71203800-71209000	Strong transcription	Liver	Liver
47	chr14:71204000-71209400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr14:71204000-71209400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr14:71204400-71209400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr14:71204800-71229400	Weak transcription	Brain Inferior Temporal Lobe	brain

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