Variant report

Variant	rs10144612
Chromosome Location	chr14:56761044-56761045
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	chr14:56714179..56714751-chr14:56760641..56761350,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10483656	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12147737	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1427556	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17688725	0.91[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs17688801	0.81[CEU][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs17689278	0.81[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs17761563	1.00[CHD][hapmap]
rs17762499	0.81[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs17762733	0.91[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs17769788	0.95[EUR][1000 genomes]
rs17832675	0.91[CEU][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs1951955	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs2035283	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2343376	0.81[CEU][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs2343604	0.95[EUR][1000 genomes]
rs28712711	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2880615	0.81[CEU][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs3850298	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs3912203	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs4127813	0.91[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs58502917	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8018553	0.94[ASW][hapmap]
rs8020301	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs959459	0.89[AMR][1000 genomes];0.95[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	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
3	nsv1044886	chr14:56689682-56834648	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv542104	chr14:56689682-56834648	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats 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	2 gene(s)	inside rSNPs	diseases
5	nsv901978	chr14:56740554-56799997	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv901979	chr14:56740554-56802610	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10144612	ARID4A	cis	cerebellum	SCAN
rs10144612	WDHD1	cis	cerebellum	SCAN
rs10144612	KIAA0586	cis	cerebellum	SCAN
rs10144612	MAPK1IP1L	cis	cerebellum	SCAN
rs10144612	ERO1L	cis	parietal	SCAN
rs10144612	PSMC6	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56717800-56765400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr14:56735800-56765800	Weak transcription	NHLF	lung
3	chr14:56738800-56766000	Weak transcription	Brain Angular Gyrus	brain
4	chr14:56738800-56775600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr14:56740000-56764800	Weak transcription	Right Ventricle	heart
6	chr14:56741600-56766000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr14:56747000-56765400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr14:56747000-56768600	Strong transcription	Dnd41	blood
9	chr14:56748400-56762800	Weak transcription	Stomach Mucosa	stomach
10	chr14:56749000-56762400	Weak transcription	Gastric	stomach
11	chr14:56750400-56777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr14:56753200-56765400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr14:56753200-56773200	Weak transcription	Fetal Brain Male	brain
14	chr14:56753800-56765600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr14:56753800-56765800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr14:56754400-56764400	Strong transcription	Primary B cells from cord blood	blood
17	chr14:56754400-56764800	Weak transcription	Colonic Mucosa	Colon
18	chr14:56754400-56765200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr14:56754400-56765200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr14:56754600-56761200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr14:56754600-56763400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr14:56754600-56765000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr14:56754600-56765400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr14:56754600-56771200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr14:56755000-56764400	Strong transcription	Thymus	Thymus
26	chr14:56755000-56767000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr14:56755200-56762800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr14:56755200-56764400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr14:56755200-56764400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr14:56755200-56769800	Strong transcription	Primary hematopoietic stem cells	blood
31	chr14:56755400-56764800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr14:56755400-56770000	Weak transcription	Brain Substantia Nigra	brain
33	chr14:56755600-56764600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr14:56755600-56765200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr14:56755600-56765400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr14:56755600-56765400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr14:56755800-56762000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr14:56755800-56765200	Weak transcription	Liver	Liver
39	chr14:56756000-56764000	Strong transcription	Fetal Brain Female	brain
40	chr14:56756200-56761200	Weak transcription	Lung	lung
41	chr14:56756400-56765400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr14:56757400-56761800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr14:56757400-56763400	Weak transcription	Brain Hippocampus Middle	brain
44	chr14:56757400-56765000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr14:56757400-56765400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr14:56757400-56765600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr14:56757400-56773200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr14:56757600-56765000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr14:56757600-56767000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr14:56758000-56764400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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