Variant report

Variant	rs4982408
Chromosome Location	chr14:21570614-21570615
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr14:21570243-21571035	K562	blood:	n/a	n/a
2	SMARCC1	chr14:21570347-21573203	Hela-S3	cervix:	n/a	chr14:21572210-21572219 chr14:21571815-21571824
3	MAX	chr14:21570425-21572898	Hela-S3	cervix:	n/a	chr14:21572210-21572219
4	JUND	chr14:21570193-21570976	K562	blood:	n/a	chr14:21570368-21570379

No.	Distal block	Cell Line	Cell type
1	chr14:21490094..21494864-chr14:21570311..21573560,5	MCF-7	breast:
2	chr14:21557595..21561276-chr14:21569876..21572764,3	K562	blood:
3	chr14:21548790..21550824-chr14:21570326..21573166,2	MCF-7	breast:
4	chr14:21535299..21541334-chr14:21568487..21576770,16	MCF-7	breast:
5	chr14:21535250..21540469-chr14:21570413..21576715,8	K562	blood:
6	chr14:21535130..21541812-chr14:21564802..21576767,22	MCF-7	breast:
7	chr14:21541693..21544085-chr14:21569593..21572197,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NDRG2-5	chr14:21569863-21572375	NONHSAT035657

Variant related genes	Relation type
ZNF219	TF binding region
ENSG00000179636	Chromatin interaction
ENSG00000165801	Chromatin interaction
ENSG00000258604	Chromatin interaction
ENSG00000165795	Chromatin interaction
ENSG00000258714	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10872886	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11156853	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11628703	0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12893688	0.91[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.86[ASN][1000 genomes]
rs4982410	0.83[CHB][hapmap]
rs745696	0.83[CHB][hapmap]
rs8010018	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8021387	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530009	chr14:21377022-22044608	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
2	nsv530769	chr14:21407536-22139126	Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv916319	chr14:21507092-21896590	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1036762	chr14:21507093-22101805	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv541976	chr14:21507093-22101805	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv826882	chr14:21511021-21604201	Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv530770	chr14:21526410-21852363	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
8	nsv525724	chr14:21540863-21574690	Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription 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	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4982408	OR6S1	cis	cerebellum	SCAN
rs4982408	PRMT5	cis	cerebellum	SCAN
rs4982408	OR4K14	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:21567400-21571400	Weak transcription	Small Intestine	intestine
2	chr14:21567400-21571400	Enhancers	Stomach Mucosa	stomach
3	chr14:21567400-21571600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr14:21567600-21570800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr14:21567600-21571400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr14:21567800-21570800	Weak transcription	Liver	Liver
7	chr14:21567800-21571000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr14:21567800-21571200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr14:21567800-21571200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr14:21567800-21571200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr14:21567800-21571200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr14:21567800-21571400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr14:21567800-21571400	Weak transcription	Primary T cells from cord blood	blood
14	chr14:21567800-21571400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr14:21567800-21571400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr14:21567800-21571400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr14:21567800-21571400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr14:21567800-21571400	Enhancers	Esophagus	oesophagus
19	chr14:21567800-21571400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr14:21567800-21571400	Weak transcription	Left Ventricle	heart
21	chr14:21567800-21571400	Weak transcription	Psoas Muscle	Psoas
22	chr14:21567800-21571400	Weak transcription	Right Ventricle	heart
23	chr14:21567800-21571600	Weak transcription	Aorta	Aorta
24	chr14:21567800-21571600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr14:21567800-21572000	Weak transcription	Ovary	ovary
26	chr14:21568000-21570800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr14:21568000-21570800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr14:21568000-21570800	Weak transcription	Fetal Brain Female	brain
29	chr14:21568000-21570800	Weak transcription	Fetal Stomach	stomach
30	chr14:21568000-21571000	Weak transcription	Placenta	Placenta
31	chr14:21568000-21571200	Weak transcription	Brain Substantia Nigra	brain
32	chr14:21568000-21571200	Weak transcription	Fetal Brain Male	brain
33	chr14:21568000-21571200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr14:21568000-21571400	Weak transcription	Right Atrium	heart
35	chr14:21568200-21570800	Weak transcription	Brain Germinal Matrix	brain
36	chr14:21568200-21570800	Weak transcription	Brain Hippocampus Middle	brain
37	chr14:21568200-21571000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr14:21568200-21571000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr14:21568200-21571000	Weak transcription	Adipose Nuclei	Adipose
40	chr14:21568200-21571200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr14:21568200-21571200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr14:21568200-21571400	Weak transcription	Fetal Kidney	kidney
43	chr14:21568400-21571200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr14:21568400-21571200	Weak transcription	Pancreas	Pancrea
45	chr14:21568600-21570800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr14:21568600-21570800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr14:21569200-21571000	Enhancers	Fetal Thymus	thymus
48	chr14:21569400-21571800	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr14:21569600-21570800	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr14:21569600-21571200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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