Variant report

Variant	rs12590049
Chromosome Location	chr14:71256367-71256368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:71254174..71260054-chr14:71263244..71266960,6	MCF-7	breast:
2	chr14:71253814..71258557-chr14:71260999..71264904,5	MCF-7	breast:
3	chr14:71255787..71258054-chr14:71274426..71275952,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006432	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10083428	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10483834	0.81[MEX][hapmap]
rs11622867	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs11626707	0.81[ASW][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs12586899	0.94[CHD][hapmap]
rs1548584	0.81[EUR][1000 genomes]
rs17108442	0.87[CHD][hapmap]
rs17108546	1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs17176985	0.81[EUR][1000 genomes]
rs17177014	0.81[EUR][1000 genomes]
rs17177097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177187	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs17766512	0.81[EUR][1000 genomes]
rs17766621	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs17766661	0.80[EUR][1000 genomes]
rs1859460	0.80[EUR][1000 genomes]
rs1859461	0.80[EUR][1000 genomes]
rs1859462	0.88[EUR][1000 genomes]
rs2023954	0.81[EUR][1000 genomes]
rs2269946	0.94[CHD][hapmap]
rs2286053	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs35506365	0.81[ASN][1000 genomes]
rs4902856	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs4902857	0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4902858	0.81[EUR][1000 genomes]
rs4902859	0.81[EUR][1000 genomes]
rs55717811	1.00[ASN][1000 genomes]
rs55881198	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56327470	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57284652	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57843652	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60533515	0.82[AMR][1000 genomes]
rs61990476	0.81[EUR][1000 genomes]
rs61990481	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61990519	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61990521	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61990523	0.81[EUR][1000 genomes]
rs7151024	0.80[EUR][1000 genomes]
rs8006715	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8022621	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS 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 miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1049741	chr14:71233043-71462509	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12590049	HEATR4	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71220800-71266400	Weak transcription	Fetal Intestine Large	intestine
2	chr14:71222200-71258200	Weak transcription	HepG2	liver
3	chr14:71222600-71274600	Weak transcription	Hela-S3	cervix
4	chr14:71223000-71258400	Weak transcription	Primary T cells from cord blood	blood
5	chr14:71223000-71266600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:71224000-71258000	Weak transcription	Dnd41	blood
7	chr14:71227800-71257800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr14:71228000-71258000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr14:71228000-71258000	Weak transcription	A549	lung
10	chr14:71228200-71258000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr14:71238600-71266600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr14:71239000-71258000	Weak transcription	Fetal Intestine Small	intestine
13	chr14:71239000-71269600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr14:71239200-71258200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr14:71239400-71258200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr14:71239800-71258400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr14:71240000-71258000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr14:71240200-71257800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr14:71240600-71258000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr14:71242400-71258200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr14:71242400-71266600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr14:71242600-71266200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr14:71246200-71258000	Weak transcription	Brain Germinal Matrix	brain
24	chr14:71246800-71266800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr14:71247000-71258200	Weak transcription	Liver	Liver
26	chr14:71247400-71266600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr14:71247600-71256600	Weak transcription	Placenta	Placenta
28	chr14:71247800-71274600	Weak transcription	Stomach Mucosa	stomach
29	chr14:71248200-71258000	Weak transcription	Gastric	stomach
30	chr14:71248200-71258000	Weak transcription	Pancreas	Pancrea
31	chr14:71248200-71271200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr14:71248800-71257400	Weak transcription	Primary B cells from cord blood	blood
33	chr14:71249000-71266400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr14:71249400-71266200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr14:71249400-71266600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr14:71249400-71266600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr14:71249400-71274400	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr14:71249400-71274400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr14:71249400-71274600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr14:71249600-71258600	Weak transcription	GM12878-XiMat	blood
41	chr14:71249600-71274600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr14:71249800-71274600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr14:71250400-71266600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr14:71252000-71262800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr14:71252200-71258000	Weak transcription	Fetal Brain Female	brain
46	chr14:71252200-71258200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr14:71252400-71256600	Weak transcription	Lung	lung
48	chr14:71252400-71258000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr14:71252600-71256800	Weak transcription	Esophagus	oesophagus
50	chr14:71252600-71268400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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