Variant report

Variant	rs242406
Chromosome Location	chr14:56615178-56615179
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:56608539..56610800-chr14:56613943..56615477,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1028972	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1152473	0.89[CEU][hapmap];0.84[CHB][hapmap];0.94[EUR][1000 genomes]
rs1152474	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[EUR][1000 genomes]
rs1152476	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[EUR][1000 genomes]
rs1152481	0.94[EUR][1000 genomes]
rs1152483	0.94[EUR][1000 genomes]
rs1188692	0.94[EUR][1000 genomes]
rs1479752	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs171411	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1979420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs242385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs242390	0.80[AMR][1000 genomes]
rs242393	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs242395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs242398	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs242407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242410	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs242414	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs242417	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs242419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs242579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes]
rs242587	0.94[EUR][1000 genomes]
rs242588	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[EUR][1000 genomes]
rs242592	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes]
rs242593	0.94[EUR][1000 genomes]
rs242594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes]
rs34175054	0.94[EUR][1000 genomes]
rs375156	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes]
rs3783668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs402332	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs429676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes]
rs6573087	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7140808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs7153057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7153858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs753109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs754689	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs754690	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs899603	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]

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	nsv533129	chr14:56568535-56819234	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats 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	5 gene(s)	inside rSNPs	diseases
2	esv1844788	chr14:56594420-56771207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56606800-56615200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr14:56609600-56615400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr14:56611400-56620000	Enhancers	Colon Smooth Muscle	Colon
4	chr14:56611800-56615800	Enhancers	Ovary	ovary
5	chr14:56612200-56617000	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr14:56612200-56618000	Enhancers	Rectal Smooth Muscle	rectum
7	chr14:56612800-56617600	Enhancers	Brain Angular Gyrus	brain
8	chr14:56613000-56615200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr14:56613000-56615400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr14:56613200-56620000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr14:56613400-56615200	Weak transcription	Brain Hippocampus Middle	brain
12	chr14:56613400-56616600	Enhancers	Fetal Brain Female	brain
13	chr14:56613400-56620000	Weak transcription	HUVEC	blood vessel
14	chr14:56613600-56616600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr14:56613600-56617800	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr14:56613600-56619800	Enhancers	Fetal Brain Male	brain
17	chr14:56613800-56615600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr14:56613800-56616000	Enhancers	Duodenum Mucosa	Duodenum
19	chr14:56613800-56618200	Enhancers	Primary hematopoietic stem cells	blood
20	chr14:56613800-56619400	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr14:56614000-56615400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr14:56614000-56615600	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr14:56614000-56616000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr14:56614000-56617000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr14:56614200-56615600	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr14:56614200-56618800	Enhancers	Primary T cells from cord blood	blood
27	chr14:56614400-56616000	Enhancers	Primary B cells from peripheral blood	blood
28	chr14:56614400-56617000	Enhancers	Primary B cells from cord blood	blood
29	chr14:56614600-56615200	Enhancers	Hela-S3	cervix
30	chr14:56614600-56615600	Enhancers	Fetal Kidney	kidney
31	chr14:56614600-56615600	Enhancers	Gastric	stomach
32	chr14:56614600-56615600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr14:56614600-56615600	Enhancers	Small Intestine	intestine
34	chr14:56614600-56615800	Enhancers	Brain Anterior Caudate	brain
35	chr14:56614600-56615800	Enhancers	Stomach Mucosa	stomach
36	chr14:56614600-56616200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr14:56614600-56616200	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr14:56614600-56616200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr14:56614600-56616600	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr14:56614600-56617000	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr14:56614600-56617200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr14:56614600-56617800	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr14:56614600-56618400	Flanking Active TSS	Dnd41	blood
44	chr14:56614600-56619000	Enhancers	Fetal Thymus	thymus
45	chr14:56614800-56615200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr14:56614800-56615200	Weak transcription	A549	lung
47	chr14:56614800-56615600	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr14:56614800-56615800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr14:56614800-56615800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr14:56614800-56615800	Enhancers	Brain Substantia Nigra	brain

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