Variant report

Variant	rs3209079
Chromosome Location	chr14:77745193-77745194
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:77741494..77746628-chr14:77751488..77756217,6	MCF-7	breast:
2	chr14:77744963..77747141-chr14:77762245..77764781,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NGB-1	chr14:77745072-77745212	NONHSAT037969

Variant related genes	Relation type
ENSG00000009830	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10132619	0.86[CHB][hapmap]
rs1017186	0.86[CHB][hapmap]
rs1046428	0.86[CHB][hapmap]
rs11850308	0.86[CHB][hapmap]
rs11850771	0.86[CHB][hapmap]
rs12894594	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12894718	0.86[CHB][hapmap]
rs1468951	0.86[CHB][hapmap]
rs1861888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs2111700	0.86[CHB][hapmap]
rs2160838	0.86[CHB][hapmap]
rs2270419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2363640	0.88[CHB][hapmap]
rs2364155	0.86[CHB][hapmap]
rs369202	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3759731	0.86[CHB][hapmap]
rs3815625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs383064	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4141640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs451925	0.93[CEU][hapmap];0.88[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4899649	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[AMR][1000 genomes]
rs4903566	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs9671248	0.86[CHB][hapmap]
rs972725	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[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	nsv431017	chr14:76938089-77854647	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv1361	chr14:77707417-77753024	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv902104	chr14:77720741-77756321	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77738800-77749600	Weak transcription	NHDF-Ad	bronchial
2	chr14:77739000-77749800	Weak transcription	HUVEC	blood vessel
3	chr14:77739400-77745400	Weak transcription	Fetal Lung	lung
4	chr14:77739400-77749000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr14:77739600-77745400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr14:77739600-77745600	Weak transcription	Primary B cells from cord blood	blood
7	chr14:77739600-77775600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr14:77740000-77749600	Weak transcription	HMEC	breast
9	chr14:77740200-77746400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr14:77740200-77749600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr14:77740200-77750800	Weak transcription	Fetal Thymus	thymus
12	chr14:77740200-77766800	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr14:77740200-77769800	Weak transcription	Small Intestine	intestine
14	chr14:77740400-77746200	Weak transcription	NHEK	skin
15	chr14:77740400-77749200	Weak transcription	Osteobl	bone
16	chr14:77740400-77766000	Weak transcription	Stomach Mucosa	stomach
17	chr14:77740800-77758000	Strong transcription	Fetal Stomach	stomach
18	chr14:77740800-77766200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr14:77741000-77749600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr14:77741000-77750000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr14:77741000-77750400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr14:77741000-77767400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr14:77741200-77745200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr14:77741200-77749400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr14:77741400-77753600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr14:77741800-77746600	Strong transcription	Brain Germinal Matrix	brain
27	chr14:77741800-77749000	Strong transcription	Fetal Intestine Small	intestine
28	chr14:77741800-77749400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr14:77741800-77752000	Weak transcription	Psoas Muscle	Psoas
30	chr14:77741800-77755400	Strong transcription	Fetal Muscle Leg	muscle
31	chr14:77741800-77757200	Strong transcription	Liver	Liver
32	chr14:77741800-77758600	Strong transcription	Fetal Muscle Trunk	muscle
33	chr14:77741800-77773600	Weak transcription	GM12878-XiMat	blood
34	chr14:77742000-77747800	Weak transcription	HSMM	muscle
35	chr14:77742000-77749200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr14:77742000-77749400	Weak transcription	NH-A	brain
37	chr14:77742000-77756800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr14:77742000-77757400	Weak transcription	Right Atrium	heart
39	chr14:77742000-77766600	Strong transcription	Placenta	Placenta
40	chr14:77742200-77748400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr14:77742200-77755000	Strong transcription	Lung	lung
42	chr14:77742200-77757600	Strong transcription	Ovary	ovary
43	chr14:77742200-77767600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr14:77742400-77745800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr14:77742400-77746000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr14:77742400-77747000	Strong transcription	Right Ventricle	heart
47	chr14:77742400-77747000	Strong transcription	Spleen	Spleen
48	chr14:77742400-77752200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr14:77742400-77753000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr14:77742400-77755000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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