Variant report

Variant	rs1980609
Chromosome Location	chr14:39780462-39780463
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	chr14:39769729..39772200-chr14:39779673..39781818,3	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10137623	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10150967	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11622951	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12433610	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1570131	0.90[ASW][hapmap]
rs1570133	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1998193	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs2025027	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs2025028	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs28502509	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs35530272	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4902459	0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs4902469	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6571912	0.82[ASW][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs6571921	0.85[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs7141840	0.95[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs7143942	1.00[ASW][hapmap]
rs7146146	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7153074	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7153523	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs8006182	1.00[ASW][hapmap]
rs8018990	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9322996	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39738200-39813800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr14:39749400-39785400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr14:39752600-39808200	Weak transcription	Stomach Mucosa	stomach
4	chr14:39755400-39783400	Strong transcription	Liver	Liver
5	chr14:39755600-39797200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr14:39756000-39788600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr14:39756200-39828400	Weak transcription	Brain Germinal Matrix	brain
8	chr14:39756600-39819600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr14:39756800-39797800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr14:39757000-39783400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr14:39757400-39796000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr14:39757400-39843800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr14:39759400-39801800	Weak transcription	NHLF	lung
14	chr14:39762400-39801600	Weak transcription	Fetal Brain Male	brain
15	chr14:39764000-39786200	Weak transcription	Brain Substantia Nigra	brain
16	chr14:39764400-39785400	Weak transcription	Esophagus	oesophagus
17	chr14:39764600-39785600	Weak transcription	Gastric	stomach
18	chr14:39764600-39785600	Weak transcription	Psoas Muscle	Psoas
19	chr14:39764600-39790000	Weak transcription	Fetal Brain Female	brain
20	chr14:39764600-39808200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr14:39764600-39818400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr14:39764800-39802400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr14:39764800-39805200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr14:39765000-39785800	Weak transcription	Lung	lung
25	chr14:39765400-39785600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr14:39765600-39789400	Weak transcription	HMEC	breast
27	chr14:39765600-39803800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr14:39765600-39807800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr14:39765800-39785400	Weak transcription	Brain Angular Gyrus	brain
30	chr14:39766000-39783000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr14:39766800-39790600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr14:39766800-39791800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr14:39767000-39785400	Weak transcription	Aorta	Aorta
34	chr14:39767000-39785400	Weak transcription	Ovary	ovary
35	chr14:39767000-39785400	Weak transcription	Spleen	Spleen
36	chr14:39767000-39785600	Weak transcription	Fetal Muscle Leg	muscle
37	chr14:39767000-39796000	Weak transcription	Thymus	Thymus
38	chr14:39767200-39801400	Weak transcription	Brain Hippocampus Middle	brain
39	chr14:39767200-39801600	Weak transcription	Right Ventricle	heart
40	chr14:39767200-39833800	Weak transcription	Small Intestine	intestine
41	chr14:39767400-39785200	Weak transcription	Brain Anterior Caudate	brain
42	chr14:39767600-39785400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr14:39768800-39785200	Weak transcription	NHEK	skin
44	chr14:39769600-39785600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr14:39769800-39796000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr14:39769800-39796000	Weak transcription	Dnd41	blood
47	chr14:39769800-39808000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr14:39770000-39816400	Weak transcription	Colon Smooth Muscle	Colon
49	chr14:39770600-39783200	Weak transcription	Fetal Intestine Small	intestine
50	chr14:39770600-39786000	Weak transcription	Fetal Stomach	stomach

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