Variant report

Variant	rs4899371
Chromosome Location	chr14:71269111-71269112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:71251307..71253279-chr14:71267106..71269549,2	MCF-7	breast:
2	chr14:71265603..71269219-chr14:71272232..71276913,5	MCF-7	breast:
3	chr14:71130975..71133007-chr14:71267977..71270888,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006432	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10129495	0.83[MEX][hapmap]
rs10134929	0.83[CHB][hapmap]
rs10139774	0.83[CHB][hapmap]
rs10141804	0.83[MEX][hapmap]
rs10873240	0.83[ASN][1000 genomes]
rs10873243	0.83[MEX][hapmap]
rs11620710	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11621269	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11622867	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11624934	0.83[MEX][hapmap]
rs11626707	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs12433469	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12437256	0.83[ASN][1000 genomes]
rs12883087	0.87[ASN][1000 genomes]
rs12883244	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs12886990	0.83[MEX][hapmap]
rs1548585	0.84[ASN][1000 genomes]
rs17108510	0.86[ASN][1000 genomes]
rs2158528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2158530	0.83[MEX][hapmap]
rs2332457	0.95[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs34307438	0.83[ASN][1000 genomes]
rs35438375	0.87[ASN][1000 genomes]
rs36025596	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902843	0.83[MEX][hapmap]
rs4902846	0.83[MEX][hapmap]
rs4902847	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4902848	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];0.82[ASN][1000 genomes]
rs4902855	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6573976	0.86[CHB][hapmap]
rs6573979	0.83[ASN][1000 genomes]
rs7151405	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7153775	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7154907	0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7160912	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7161415	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72721934	0.87[ASN][1000 genomes]
rs8005459	0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs8019156	0.82[CEU][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8019513	0.83[MEX][hapmap]
rs8022269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8022410	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8022803	0.86[ASN][1000 genomes]
rs886600	0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs9323548	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4899371	DNAL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71222600-71274600	Weak transcription	Hela-S3	cervix
2	chr14:71239000-71269600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:71247800-71274600	Weak transcription	Stomach Mucosa	stomach
4	chr14:71248200-71271200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr14:71249400-71274400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr14:71249400-71274400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr14:71249400-71274600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr14:71249600-71274600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr14:71249800-71274600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr14:71256600-71269600	Weak transcription	Brain Hippocampus Middle	brain
11	chr14:71257200-71274600	Weak transcription	Brain Anterior Caudate	brain
12	chr14:71257200-71274600	Weak transcription	Spleen	Spleen
13	chr14:71257800-71274800	Weak transcription	Colonic Mucosa	Colon
14	chr14:71259000-71274600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr14:71260000-71274800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr14:71261200-71270400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr14:71261200-71270600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr14:71261200-71271400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr14:71261200-71274600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr14:71261600-71272000	Weak transcription	Fetal Stomach	stomach
21	chr14:71265000-71274600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr14:71265200-71274600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr14:71265800-71274600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr14:71267400-71274600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr14:71267600-71269600	Weak transcription	Primary B cells from cord blood	blood
26	chr14:71267600-71270600	Weak transcription	Primary T cells from cord blood	blood
27	chr14:71267600-71272400	Weak transcription	Fetal Intestine Large	intestine
28	chr14:71267600-71272800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr14:71267600-71274400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr14:71267600-71274400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr14:71267600-71274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr14:71267600-71274600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr14:71267600-71274600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr14:71267600-71274600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr14:71267600-71274600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr14:71267600-71274600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr14:71267800-71269200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr14:71267800-71270200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr14:71267800-71270400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr14:71267800-71270600	Weak transcription	Liver	Liver
41	chr14:71267800-71271200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr14:71267800-71271600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr14:71267800-71273800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr14:71267800-71274400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr14:71267800-71274400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr14:71267800-71274400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr14:71267800-71274400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr14:71267800-71274400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr14:71267800-71274400	Weak transcription	Brain Germinal Matrix	brain
50	chr14:71267800-71274400	Weak transcription	Fetal Brain Female	brain

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