Variant report

Variant	rs10135215
Chromosome Location	chr14:21947857-21947858
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:21922608..21930261-chr14:21941288..21947915,21	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100888	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1060722	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061031	0.86[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs11156994	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1139130	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12431578	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12435421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1263791	1.00[CEU][hapmap]
rs1263793	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1263796	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1263799	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1263801	0.96[CEU][hapmap];0.81[AMR][1000 genomes]
rs12880402	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12889546	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2282046	0.81[TSI][hapmap];0.93[YRI][hapmap]
rs2297093	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28526734	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28608673	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28694613	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737050	0.86[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs4296176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6571850	0.86[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs6571851	0.80[ASN][1000 genomes]
rs7150948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8004916	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs933192	0.87[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs966602	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530009	chr14:21377022-22044608	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
2	nsv530769	chr14:21407536-22139126	Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv1036762	chr14:21507093-22101805	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv541976	chr14:21507093-22101805	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	esv3518898	chr14:21805983-22077584	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	esv3518899	chr14:21805983-22077584	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv1054013	chr14:21868964-21992109	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv541991	chr14:21868964-21992109	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv530011	chr14:21876973-21985341	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv2422459	chr14:21931624-22169502	Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	esv994931	chr14:21947144-21956367	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10135215	METTL3	cis	lymphoblastoid	seeQTL
rs10135215	RAB2B	cis	multi-tissue	Pritchard
rs10135215	LTB4R	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:21946000-21960600	Weak transcription	Small Intestine	intestine
2	chr14:21946200-21949200	Weak transcription	Esophagus	oesophagus
3	chr14:21946200-21949200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr14:21946200-21955600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:21946200-21955600	Weak transcription	Gastric	stomach
6	chr14:21946200-21955600	Weak transcription	Left Ventricle	heart
7	chr14:21946200-21955600	Weak transcription	Ovary	ovary
8	chr14:21946200-21955600	Weak transcription	Thymus	Thymus
9	chr14:21946200-21977600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr14:21946400-21948200	Weak transcription	HSMM	muscle
11	chr14:21946400-21948800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr14:21946400-21952000	Weak transcription	Lung	lung
13	chr14:21946400-21952600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr14:21946400-21952800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr14:21946400-21955400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr14:21946400-21955600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr14:21946400-21958000	Weak transcription	Pancreas	Pancrea
18	chr14:21946400-21958800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr14:21946400-21960800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr14:21946400-21971400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr14:21946600-21948000	Weak transcription	Placenta	Placenta
22	chr14:21946600-21949200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr14:21946600-21949200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr14:21946600-21949400	Weak transcription	Brain Anterior Caudate	brain
25	chr14:21946600-21949400	Weak transcription	Fetal Kidney	kidney
26	chr14:21946600-21949600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr14:21946600-21950400	Weak transcription	Primary B cells from cord blood	blood
28	chr14:21946600-21954600	Weak transcription	HSMMtube	muscle
29	chr14:21946600-21954800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr14:21946600-21954800	Weak transcription	K562	blood
31	chr14:21946600-21955000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr14:21946600-21955000	Weak transcription	Fetal Thymus	thymus
33	chr14:21946600-21955400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr14:21946600-21955400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr14:21946600-21955600	Weak transcription	Brain Germinal Matrix	brain
36	chr14:21946600-21955600	Weak transcription	Colonic Mucosa	Colon
37	chr14:21946600-21955600	Weak transcription	Fetal Muscle Leg	muscle
38	chr14:21946600-21955600	Weak transcription	Psoas Muscle	Psoas
39	chr14:21946600-21955600	Weak transcription	Right Ventricle	heart
40	chr14:21946600-21955600	Weak transcription	Spleen	Spleen
41	chr14:21946600-21955800	Weak transcription	Fetal Brain Female	brain
42	chr14:21946600-21958000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr14:21946600-21960400	Weak transcription	Stomach Mucosa	stomach
44	chr14:21946600-21960800	Weak transcription	Aorta	Aorta
45	chr14:21946800-21948000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr14:21946800-21949400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr14:21946800-21949400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr14:21946800-21950200	Weak transcription	NHLF	lung
49	chr14:21946800-21950400	Weak transcription	NHDF-Ad	bronchial
50	chr14:21946800-21954600	Weak transcription	Brain Hippocampus Middle	brain

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