Variant report

Variant	rs4899672
Chromosome Location	chr14:78158063-78158064
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:78156716..78160622-chr14:78162116..78165748,3	K562	blood:
2	chr14:78157152..78158928-chr14:78163519..78165919,2	MCF-7	breast:
3	chr14:78136536..78139253-chr14:78155471..78158284,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258917	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1030151	1.00[CEU][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1030152	0.88[EUR][1000 genomes]
rs17106259	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17106364	0.83[EUR][1000 genomes]
rs17752135	0.88[CEU][hapmap]
rs45519831	0.88[EUR][1000 genomes]
rs45611739	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4899669	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4899671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4903628	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4903630	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4903633	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs57485881	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57654091	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58390480	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61435552	0.88[EUR][1000 genomes]
rs61990683	0.86[EUR][1000 genomes]
rs61990684	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61990686	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61990688	0.83[EUR][1000 genomes]
rs61990689	0.83[EUR][1000 genomes]
rs61990690	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61990695	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61990716	0.83[EUR][1000 genomes]
rs61990717	0.83[EUR][1000 genomes]
rs61990718	0.83[EUR][1000 genomes]
rs61990721	0.80[EUR][1000 genomes]
rs61990722	0.80[EUR][1000 genomes]
rs61990855	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61990856	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61992865	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61992869	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61992870	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61992912	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61992917	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61992919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61992921	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61993669	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61993672	0.89[EUR][1000 genomes]
rs6574390	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7143265	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7143382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7146446	0.83[EUR][1000 genomes]
rs7147748	1.00[EUR][1000 genomes]
rs7152638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7156186	1.00[CEU][hapmap];0.94[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7156905	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7160307	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8007598	0.88[EUR][1000 genomes]
rs8014720	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8019064	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	esv2757575	chr14:78104897-78212462	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv34940	chr14:78104897-78222798	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv521287	chr14:78108003-78211225	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv869872	chr14:78119527-78161340	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv520021	chr14:78152921-78208294	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4899672	RPL21P10	cis	Muscle Skeletal	GTEx
rs4899672	RPL21P10	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78127400-78173200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:78134400-78163400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:78136200-78162800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:78137800-78161200	Weak transcription	Fetal Heart	heart
5	chr14:78138000-78171800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr14:78140400-78160400	Weak transcription	Fetal Kidney	kidney
7	chr14:78140400-78172400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr14:78140600-78158600	Weak transcription	Esophagus	oesophagus
9	chr14:78140600-78173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:78141200-78160400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr14:78141200-78162800	Weak transcription	Colonic Mucosa	Colon
12	chr14:78142200-78161200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr14:78142600-78162200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr14:78142600-78162800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr14:78145400-78158600	Weak transcription	Spleen	Spleen
16	chr14:78146400-78160000	Weak transcription	Brain Hippocampus Middle	brain
17	chr14:78146400-78161800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr14:78148200-78158600	Weak transcription	Gastric	stomach
19	chr14:78148400-78158400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr14:78148400-78158600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr14:78148400-78162800	Weak transcription	Aorta	Aorta
22	chr14:78148400-78162800	Weak transcription	Pancreas	Pancrea
23	chr14:78148400-78164400	Weak transcription	Psoas Muscle	Psoas
24	chr14:78148600-78158200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr14:78148600-78158400	Weak transcription	Colon Smooth Muscle	Colon
26	chr14:78148600-78162800	Weak transcription	NHLF	lung
27	chr14:78149000-78158400	Weak transcription	NHEK	skin
28	chr14:78149000-78160400	Weak transcription	Hela-S3	cervix
29	chr14:78149200-78163800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr14:78149200-78171400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr14:78149800-78158600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr14:78149800-78163000	Weak transcription	Stomach Mucosa	stomach
33	chr14:78149800-78164200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr14:78150200-78163800	Strong transcription	Fetal Muscle Leg	muscle
35	chr14:78150400-78172200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr14:78152200-78158800	Weak transcription	Fetal Intestine Small	intestine
37	chr14:78152200-78164200	Strong transcription	Liver	Liver
38	chr14:78152200-78164600	Strong transcription	Adipose Nuclei	Adipose
39	chr14:78152400-78171200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr14:78152600-78172200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr14:78152800-78158200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr14:78152800-78165400	Strong transcription	Placenta	Placenta
43	chr14:78152800-78171400	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr14:78153400-78163000	Weak transcription	Right Ventricle	heart
45	chr14:78153400-78171200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr14:78153400-78171400	Strong transcription	Primary B cells from peripheral blood	blood
47	chr14:78153400-78172000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr14:78153800-78158400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr14:78154200-78158200	Weak transcription	Lung	lung
50	chr14:78154400-78159000	Strong transcription	Fetal Stomach	stomach

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