Variant report

Variant	rs2332457
Chromosome Location	chr14:71215380-71215381
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:71214355..71216029-chr14:71274395..71276069,2	MCF-7	breast:
2	chr14:71209875..71213128-chr14:71214251..71217560,3	K562	blood:
3	chr14:71214804..71217337-chr14:71274832..71276743,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006432	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10134929	0.87[CHB][hapmap]
rs10139774	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs10873240	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11620710	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11621269	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11622867	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11622989	0.83[ASW][hapmap];0.88[MEX][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11626707	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs11852001	0.86[ASN][1000 genomes]
rs12433469	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12437037	0.86[ASN][1000 genomes]
rs12437256	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12883087	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12883244	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12895576	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1548585	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17108510	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2158528	0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs34307438	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35438375	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36025596	0.83[ASN][1000 genomes]
rs4899371	0.95[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4902847	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902848	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902855	0.95[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs61359483	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6573976	0.91[CHB][hapmap]
rs6573979	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7147731	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7151405	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7153775	0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs7154907	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7160912	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7161415	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72721934	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8005459	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8006539	0.83[CHB][hapmap];0.93[CHD][hapmap]
rs8014356	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8014624	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8022269	0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs8022410	0.82[ASN][1000 genomes]
rs8022803	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs886600	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2332457	DNAL1	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71185800-71219200	Weak transcription	Stomach Mucosa	stomach
2	chr14:71186000-71221600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:71186000-71221600	Weak transcription	Hela-S3	cervix
4	chr14:71191400-71220000	Weak transcription	Fetal Brain Male	brain
5	chr14:71191600-71220200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr14:71192400-71220200	Weak transcription	Fetal Kidney	kidney
7	chr14:71192600-71221800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr14:71194000-71222000	Weak transcription	HSMMtube	muscle
9	chr14:71194400-71221600	Weak transcription	Left Ventricle	heart
10	chr14:71194600-71218600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr14:71194600-71221600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr14:71196200-71217000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr14:71197000-71228800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr14:71197600-71217000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr14:71198400-71223400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr14:71199600-71219600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr14:71200200-71216400	Weak transcription	Brain Hippocampus Middle	brain
18	chr14:71200400-71215400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr14:71200600-71224200	Weak transcription	Spleen	Spleen
20	chr14:71201200-71228000	Weak transcription	Colonic Mucosa	Colon
21	chr14:71201600-71219000	Weak transcription	Lung	lung
22	chr14:71201600-71220600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr14:71204800-71229400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr14:71205000-71219000	Weak transcription	Brain Angular Gyrus	brain
25	chr14:71205400-71220400	Weak transcription	Small Intestine	intestine
26	chr14:71206000-71218200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr14:71206800-71221000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr14:71206800-71231600	Weak transcription	Brain Anterior Caudate	brain
29	chr14:71207000-71215400	Weak transcription	GM12878-XiMat	blood
30	chr14:71207000-71221800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr14:71207000-71221800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr14:71209000-71215400	Weak transcription	Liver	Liver
33	chr14:71209200-71215400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr14:71209200-71229400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr14:71209400-71219000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr14:71209400-71219000	Weak transcription	Gastric	stomach
37	chr14:71209400-71219400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr14:71209400-71221600	Weak transcription	Esophagus	oesophagus
39	chr14:71209400-71238200	Weak transcription	Fetal Stomach	stomach
40	chr14:71209400-71238400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr14:71209400-71238400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr14:71209600-71229000	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr14:71210800-71217200	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr14:71210800-71220600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr14:71211200-71217200	Strong transcription	HMEC	breast
46	chr14:71211600-71216400	Strong transcription	Fetal Brain Female	brain
47	chr14:71211600-71217200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr14:71211800-71215600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr14:71212000-71217000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr14:71212000-71238200	Weak transcription	Fetal Intestine Small	intestine

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