Variant report

Variant	rs12879569
Chromosome Location	chr14:71194774-71194775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:71192214..71195072-chr14:71196372..71198780,2	K562	blood:
2	chr14:71189704..71191620-chr14:71192243..71194827,2	MCF-7	breast:
3	chr14:71188747..71190799-chr14:71193873..71196833,2	MCF-7	breast:
4	chr14:71193884..71195737-chr14:71203003..71205653,2	MCF-7	breast:
5	chr14:71194431..71195182-chr14:71284389..71285014,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10129307	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1034769	0.81[GIH][hapmap]
rs1476609	0.87[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs1476610	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2158526	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2158527	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2332455	0.92[CEU][hapmap]
rs3814872	0.87[ASW][hapmap];0.81[GIH][hapmap];0.81[LWK][hapmap]
rs4141095	1.00[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4899367	0.94[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4899368	0.87[ASW][hapmap];0.81[GIH][hapmap];0.81[LWK][hapmap];0.82[AFR][1000 genomes]
rs4902852	0.87[ASW][hapmap];0.81[GIH][hapmap]
rs6573978	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7152246	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8006424	0.94[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs8011047	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8011507	0.92[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12879569	SRSF5	cis	cerebellum	SCAN
rs12879569	MAP3K9	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71177200-71195600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr14:71180600-71196800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:71180600-71196800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:71180800-71196000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr14:71180800-71200800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr14:71181200-71195800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr14:71185400-71198800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr14:71185800-71196400	Weak transcription	Colonic Mucosa	Colon
9	chr14:71185800-71196600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr14:71185800-71198600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr14:71185800-71219200	Weak transcription	Stomach Mucosa	stomach
12	chr14:71186000-71195400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:71186000-71195600	Weak transcription	Pancreas	Pancrea
14	chr14:71186000-71196600	Weak transcription	Gastric	stomach
15	chr14:71186000-71196600	Weak transcription	Lung	lung
16	chr14:71186000-71221600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr14:71186000-71221600	Weak transcription	Hela-S3	cervix
18	chr14:71188000-71196800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr14:71188600-71195600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr14:71188600-71198600	Weak transcription	Liver	Liver
21	chr14:71188800-71198400	Strong transcription	HMEC	breast
22	chr14:71189600-71196000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr14:71189600-71196000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr14:71189800-71209400	Strong transcription	Fetal Brain Female	brain
25	chr14:71190000-71196200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr14:71190000-71214400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr14:71190600-71196000	Weak transcription	Brain Anterior Caudate	brain
28	chr14:71191200-71196200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr14:71191400-71220000	Weak transcription	Fetal Brain Male	brain
30	chr14:71191600-71220200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr14:71191800-71196200	Weak transcription	Brain Germinal Matrix	brain
32	chr14:71191800-71196400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr14:71191800-71198600	Weak transcription	HepG2	liver
34	chr14:71192000-71195400	Weak transcription	Esophagus	oesophagus
35	chr14:71192000-71196400	Weak transcription	Brain Angular Gyrus	brain
36	chr14:71192200-71195400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr14:71192200-71196000	Weak transcription	Fetal Intestine Large	intestine
38	chr14:71192200-71198000	Strong transcription	NHEK	skin
39	chr14:71192400-71195600	Weak transcription	Placenta	Placenta
40	chr14:71192400-71220200	Weak transcription	Fetal Kidney	kidney
41	chr14:71192600-71196600	Weak transcription	Dnd41	blood
42	chr14:71192600-71221800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr14:71193000-71195400	Weak transcription	Primary B cells from cord blood	blood
44	chr14:71193400-71211400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr14:71193600-71196000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr14:71193600-71199400	Strong transcription	A549	lung
47	chr14:71193600-71210200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr14:71193800-71196000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr14:71193800-71196400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr14:71193800-71209400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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