Variant report

Variant	rs10129495
Chromosome Location	chr14:71215729-71215730
allele	A/G
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: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10131177	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10131364	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10141804	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10143748	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10147150	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10873243	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11158882	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11621281	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624934	0.96[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];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11625206	0.91[MEX][hapmap];0.87[TSI][hapmap]
rs11625330	0.86[EUR][1000 genomes]
rs11628333	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs12886990	0.96[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];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12887479	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12888427	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12897648	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17108492	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1987652	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2158530	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2158531	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28420983	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36570	0.83[CHD][hapmap]
rs4899371	0.83[MEX][hapmap]
rs4902843	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4902846	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902849	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66736782	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71425216	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71425219	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8008802	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8019261	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8019448	1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8019513	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs8020663	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8022333	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8022401	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9323548	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10129495	MAP3K9	cis	multi-tissue	Pritchard
rs10129495	PSEN1	cis	parietal	SCAN

Chromatin state (count:84 , 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	chr14:71200600-71224200	Weak transcription	Spleen	Spleen
19	chr14:71201200-71228000	Weak transcription	Colonic Mucosa	Colon
20	chr14:71201600-71219000	Weak transcription	Lung	lung
21	chr14:71201600-71220600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr14:71204800-71229400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr14:71205000-71219000	Weak transcription	Brain Angular Gyrus	brain
24	chr14:71205400-71220400	Weak transcription	Small Intestine	intestine
25	chr14:71206000-71218200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr14:71206800-71221000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr14:71206800-71231600	Weak transcription	Brain Anterior Caudate	brain
28	chr14:71207000-71221800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr14:71207000-71221800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr14:71209200-71229400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr14:71209400-71219000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr14:71209400-71219000	Weak transcription	Gastric	stomach
33	chr14:71209400-71219400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr14:71209400-71221600	Weak transcription	Esophagus	oesophagus
35	chr14:71209400-71238200	Weak transcription	Fetal Stomach	stomach
36	chr14:71209400-71238400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr14:71209400-71238400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr14:71209600-71229000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr14:71210800-71217200	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr14:71210800-71220600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr14:71211200-71217200	Strong transcription	HMEC	breast
42	chr14:71211600-71216400	Strong transcription	Fetal Brain Female	brain
43	chr14:71211600-71217200	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr14:71212000-71217000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr14:71212000-71238200	Weak transcription	Fetal Intestine Small	intestine
46	chr14:71212400-71218800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr14:71212600-71216800	Strong transcription	Duodenum Mucosa	Duodenum
48	chr14:71212600-71220200	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr14:71212800-71217000	Strong transcription	Primary B cells from peripheral blood	blood
50	chr14:71213000-71216800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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