Variant report

Variant	rs2880615
Chromosome Location	chr14:56610653-56610654
allele	A/C
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: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10144612	0.81[CEU][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs10483656	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs1427556	0.81[CEU][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap]
rs17688725	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17688801	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17689278	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17761563	1.00[CHD][hapmap];0.90[GIH][hapmap]
rs17762499	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17762733	0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17832675	0.90[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1951955	0.89[CEU][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2035283	0.81[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2343376	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28712711	0.81[EUR][1000 genomes]
rs3850298	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3912203	0.90[CEU][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4127813	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8020301	0.81[CEU][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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2880615	ERO1L	cis	parietal	SCAN
rs2880615	C14orf37	cis	cerebellum	SCAN
rs2880615	ARID4A	cis	cerebellum	SCAN
rs2880615	PSMC6	cis	cerebellum	SCAN
rs2880615	C14orf166	cis	cerebellum	SCAN
rs2880615	MAPK1IP1L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56593200-56612800	Weak transcription	Brain Angular Gyrus	brain
2	chr14:56596600-56615000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:56597000-56611800	Weak transcription	Lung	lung
4	chr14:56599400-56614800	Weak transcription	Brain Substantia Nigra	brain
5	chr14:56599400-56615000	Weak transcription	Left Ventricle	heart
6	chr14:56600600-56615000	Weak transcription	Right Atrium	heart
7	chr14:56604200-56614800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr14:56604400-56610800	Weak transcription	Colon Smooth Muscle	Colon
9	chr14:56604800-56612000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr14:56604800-56612200	Weak transcription	Brain Hippocampus Middle	brain
11	chr14:56605800-56614200	Weak transcription	Primary T cells from cord blood	blood
12	chr14:56606000-56611800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr14:56606000-56612200	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr14:56606000-56612200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr14:56606000-56613000	Weak transcription	Fetal Thymus	thymus
16	chr14:56606000-56614000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr14:56606000-56614800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr14:56606000-56615000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr14:56606000-56615000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr14:56606000-56615000	Weak transcription	Spleen	Spleen
21	chr14:56606600-56614600	Weak transcription	Fetal Kidney	kidney
22	chr14:56606800-56613000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr14:56606800-56615200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr14:56607000-56611600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr14:56607000-56611600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr14:56607000-56611800	Weak transcription	Fetal Brain Male	brain
27	chr14:56607000-56613800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr14:56607400-56611600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr14:56607800-56613200	Enhancers	Dnd41	blood
30	chr14:56607800-56613800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr14:56607800-56614600	Weak transcription	Brain Anterior Caudate	brain
32	chr14:56607800-56614800	Weak transcription	Brain Germinal Matrix	brain
33	chr14:56608200-56611800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr14:56608200-56613200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr14:56608800-56611600	Weak transcription	Stomach Mucosa	stomach
36	chr14:56609000-56612400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr14:56609200-56611800	Weak transcription	Ovary	ovary
38	chr14:56609200-56611800	Weak transcription	Pancreas	Pancrea
39	chr14:56609200-56611800	Weak transcription	Thymus	Thymus
40	chr14:56609200-56612800	Weak transcription	Fetal Brain Female	brain
41	chr14:56609200-56614600	Weak transcription	Gastric	stomach
42	chr14:56609600-56615400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr14:56610000-56612600	Weak transcription	NH-A	brain
44	chr14:56610000-56614600	Weak transcription	Small Intestine	intestine
45	chr14:56610200-56610800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr14:56610400-56610800	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr14:56610400-56611200	Enhancers	Psoas Muscle	Psoas
48	chr14:56610400-56612400	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr14:56610600-56611200	Enhancers	Rectal Smooth Muscle	rectum
50	chr14:56610600-56612000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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